Showing posts with label East Pacific Rise. Show all posts
Showing posts with label East Pacific Rise. Show all posts

Saturday, 3 January 2026

Magnitude 6.5 Earthquake in Guerrero State, Mexico.

The United States Geological Survey recorded a Magnitude 6.5 Earthquake at a depth of 35.0 km, approximately 4 km to the north of the resort of Rancho Viejo in Guerrero State, slightly before 10.00 am local time (slightly before 2.00 pm GMT) on Friday 2 January 2025. This even was felt across much of southern and central Mexico, with at least two people having died, a 50-year-old woman in Guerrero State, and a 60-year-old man in Mexico City. At least 12 further people were injured by the event. 

The approximate location of the 3 January 2026 Guerrero State Earthquake. Contour lines show rates of movement during the quake, the red line is the Middle American Trench. USGS.

Mexico is located on the southernmost part of the North American Plate. To the south, along the Middle American Trench, which lies off the southern coast off Mexico, the Cocos Plate is being subducted under the North American Plate, passing under southern Mexico as it sinks into the Earth. Guatemala is located on the southern part of the Caribbean Plate, close to its boundary with the Cocos Plate, which underlies part of the east Pacific. The Cocos Plate is being pushed northwards by expansion of the crust along the East Pacific Rise, and is subducted beneath the Caribbean Plate along the Middle American Trench. This is not a smooth process, and the plates frequently stick together then break apart as the pressure builds up, causing Earthquakes in the process. 

The position of the Cocos, Nazca and Rivera Plates. MCEER/University at Buffalo.

The Cocos Plate is thought to have formed about 23 million years ago, when the Farallon Plate, an ancient tectonic plate underlying the East Pacific, split in two, forming the Cocos Plate to the north and the Nazca Plate to the south. Then, roughly 10 million years ago, the northwesternmost part of the Cocos Plate split of to form the Rivera Plate, south of Beja California.

In a paper published in the Journal of Geophysical Research, in 2012, a team led by Igor Stubailo of the Department of Earth and Space Sciences at the University of California Los Angeles, published a model of the subduction zone beneath Mexico using data from seismic monitoring stations belonging to the Mesoamerican Seismic Experiment, the Network of Autonomously Recording Seismographs, the USArray, Mapping the Rivera Subduction Zone, and the Mexican Servicio Sismologico Nacional.

The seismic monitoring stations were able to monitor not just Earthquakes in Mexico, but also Earthquakes in other parts of the world, monitoring the rate at which compression waves from these quakes moved through the rocks beneath Mexico, and how the structure of the rocks altered the movement of these waves.

Based upon the results from these monitoring stations, Stubailo et al. came to the conclusion that the Cocos Plate was split into two beneath Mexico, and that the two plates are subducting at different angles, one steep and one shallow. Since the rate at which a plate melts reflects its depth within the Earth, the steeper angled plate melts much closer to the subduction zone than the shallower angled plate, splitting the Trans-Mexican Volcanic Belt into sections above the different segments of the Cocos Plate, and causing it to apparently curve away from the subduction zone.

Top the model of the Cocos Plate beneath Mexico, split into two sections (A & B) subducting at differing angles. (C) Represents the Rivera Plate, subducting at a steeper angle than either section of the Cocos Plate. The Split between the two has been named the Orozco Fracture Zone (OFZ) which is shown extended across the Cocos Plate; in theory this might in future split the Cocos Plate into two segments (though not on any human timescale). Bottom Left, the position of the segments on a map of Mexico. Darker area is the Trans-Mexican Volcanic Belt, orange circles are volcanoes, brown triangles are seismic monitoring stations, yellow stars are major cities. Bottom Right, an alternative model showing the subducting plate twisted but not split. This did not fit the data. Stubailo et al. (2012).

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Tuesday, 14 May 2024

Magnitude 6.4 Earthquake off the coast of the Mexico/Guatemala border.

The United States Geological Survey recorded a Magnitude 6.4 Earthquake at a depth of 75.4 km, approximately 17 km off the south coast of the border between Mexico and Guatemala, slightly before 5.40 am local time (slightly before 11.40 am GMT) on Sunday 12 May 2024. This even was felt across much of southern Guatemala, and Chiapas State, Mexico, and triggered a number of small landslides as well as minor damage to some buildings, but there are no reports of any injuries.

The approximate location of the 12 May 2024 Mexico/Guatemala Earthquake. Contour lines show rates of movement during the quake, the red line is the Middle American Trench. USGS.

Mexico is located on the southernmost part of the North American Plate. To the south, along the Middle American Trench, which lies off the southern coast off Mexico, the Cocos Plate is being subducted under the North American Plate, passing under southern Mexico as it sinks into the Earth. Guatemala is located on the southern part of the Caribbean Plate, close to its boundary with the Cocos Plate, which underlies part of the east Pacific. The Cocos Plate is being pushed northwards by expansion of the crust along the East Pacific Rise, and is subducted beneath the Caribbean Plate along the Middle American Trench. This is not a smooth process, and the plates frequently stick together then break apart as the pressure builds up, causing Earthquakes on the process. 

The position of the Cocos, Nazca and Rivera Plates. MCEER/University at Buffalo.

The Cocos Plate is thought to have formed about 23 million years ago, when the Farallon Plate, an ancient tectonic plate underlying the East Pacific, split in two, forming the Cocos Plate to the north and the Nazca Plate to the south. Then, roughly 10 million years ago, the northwesternmost part of the Cocos Plate split of to form the Rivera Plate, south of Beja California.

In a paper published in the Journal of Geophysical Research, in 2012, a team led by Igor Stubailo of the Department of Earth and Space Sciences at the University of California Los Angeles, published a model of the subduction zone beneath Mexico using data from seismic monitoring stations belonging to the Mesoamerican Seismic Experiment, the Network of Autonomously Recording Seismographs, the USArray, Mapping the Rivera Subduction Zone and the Mexican Servicio Sismologico Nacional.

The seismic monitoring stations were able to monitor not just Earthquakes in Mexico, but also Earthquakes in other parts of the world, monitoring the rate at which compression waves from these quakes moved through the rocks beneath Mexico, and how the structure of the rocks altered the movement of these waves.

Based upon the results from these monitoring stations, Stubailo et al. came to the conclusion that the Cocos Plate was split into two beneath Mexico, and that the two plates are subducting at different angles, one steep and one shallow. Since the rate at which a plate melts reflects its depth within the Earth, the steeper angled plate melts much closer to the subduction zone than the shallower angled plate, splitting the Trans-Mexican Volcanic Belt into sections above the different segments of the Cocos Plate, and causing it to apparently curve away from the subduction zone.

Top the model of the Cocos Plate beneath Mexico, split into two sections (A & B) subducting at differing angles. (C) Represents the Rivera Plate, subducting at a steeper angle than either section of the Cocos Plate. The Split between the two has been named the Orozco Fracture Zone (OFZ) which is shown extended across the Cocos Plate; in theory this might in future split the Cocos Plate into two segments (though not on any human timescale). Bottom Left, the position of the segments on a map of Mexico. Darker area is the Trans-Mexican Volcanic Belt, orange circles are volcanoes, brown triangles are seismic monitoring stations, yellow stars are major cities. Bottom Right, an alternative model showing the subducting plate twisted but not split. This did not fit the data. Stubailo et al. (2012).

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Friday, 19 May 2023

Magnitude 6.4 Earthquake beneath southern Guatemala.

The United States Geological Survey Recorded a Magnitude 6.4 Earthquake at a depth of 252 km about 2 km to the southeast of the town of Canillá, in El QuichĂ© Department, Guatemala, slightly after 11.00 pm local time (slightly after 5.00 pm GMT) on Wednesday 17 May 2023. No injuries or damage have been reported following this event, but the Earthquake was felt across most of Guatemala, plus parts of southern Mexico and El Salvador. Such a pattern is typical of Earthquakes at great depth, where the energy tends ti be dispersed over a wide area by the time it reaches the surface.

The approximate location of the 17 May 2023 Guatemala Earthquake. USGS.

Guatemala is located on the southern part of the boundary between the North American and Caribbean Plates, close to their boundary with the Cocos Plate, which underlies part of the east Pacific. The Cocos Plate is being pushed northwards by expansion of the crust along the East Pacific Rise, and is subducted beneath the North American and Caribbean Plates along the Middle American Trench, which runs parallel to the south coast of Guatemala and neighbouring countries, passing under Central America as it sinks into the Earth's interior. This is not a smooth process, the plates tend to stick together, breaking apart again once the pressure from the northward movement of the Cocos Plate builds up to much, triggering Earthquakes.

Diagrammatic representation of the subduction of the Cocos Plate beneath the Caribbean Plate along the Middle American Trench. VCS Mining.

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Friday, 12 March 2021

Nitrosophilus alvini: A new species of hydrogen-oxidising chemolithoautotroph Bacterium isolated from a deep-sea hydrothermal vent in the East Pacific Rise.

The phylum 'Campylobacterota' is a phylogenetically and ecophysiologically diverse Bacterial group that consists of two classes, i.e., Desulfurellia (the former order Desulfurellales) and 'Campylobacteria' (the former class Epsilonproteobacteria). While this phylum is widely recognised as a group including pathogenic microorganisms, e.g. Helicobacter pylori and Campylobacter jejuni, and many studies have focused on these pathogens, an ever expanding number of non-pathogenic species have been identified which thrive as mesophiles or thermophiles in a wide range of natural environments (e.g. deep-sea hydrothermal fields, stratified ocean, terrestrial sulfidic caves, and oil fields) where they are recognized as important players in biogeochemical cycles. Cultivation and characterisation of these bacteria has also expanded our knowledge on the evolution and diversification of pathogenic relatives, biogeography, and the potential of biotechnological applications to mitigate global warming.

At deep-sea hydrothermal vents, Bacteria belonging to the phylum 'Campylobacterota' are known as the dominant community members, including sulphide chimney structures where they can comprise up to 85% of the microbial biomass. Taxonomically and metabolically diverse members of chemosynthetic 'Campylobacterota' are responsible for the primary production. Ever since thermophilic 'Campylobacterota' were first cultivated from hydrothermal vents, the number of culturable thermophilic members has increased with the refinement of cultivation conditions. Nevertheless, the described thermophilic species still account for only 14% of the total number of validly published species within 'Campylobacterota', and therefore there is still insufficient information on their genomes and intra-specific diversity. This also leaves the classification of thermophiles unresolved as almost all thermophilic families are composed of only a single genus, which were mostly retrieved from deepsea hydrothermal vents.

The family Nitratiruptoraceae is one of the thermophilic groups within 'Campylobacteria' that is frequently detected in deep-sea hydrothermal environments globally. This family consists so far of one validly described genus and species, Nitratiruptor tergarcus, isolated from the deep-sea hydrothermal chimney structure in the Mid-Okinawa Trough. The recently described species 'Nitratiruptor labii' was also isolated from the same deep-sea hydrothermal region. In addition to the importance of Nitratiruptoraceae species in biogeochemical cycles, their potential for industrial applications has been described. Isolation of novel Nitratiruptoraceae species and elucidation of their physiological and genomic characteristics are both necessary to help understanding the diversity of this group and the evolutionary relationships within 'Campylobacteria'.

16S rRNA gene sequences have been the universal molecular chronometer for microbial taxonomic affiliation for more than three decades, but this tool does not work well in classifying either closely related species or distantly related taxa. The rapid advances in sequencing technology over the past decade have resulted in an increase in the amount of whole genome data and have brought significant opportunities to introduce robust and accurate criteria to improve microbial taxonomy. One advance is the genome-based taxonomy based on the use of a large number of conserved core genes and indices such as in silico DNA-DNA hybridisation, average nucleotide identity, average amino acid identity, which refines phylogenetic analyses using genome sequence data. These classifiers enable the robust classification of novel species or genera, resulting in a more accurate microbial taxonomy. Genome-based methods could also be effective in classifying members within the phylum 'Campylobacterota'. However, the robust and accurate criteria using genome relatedness indices have not yet been fully evaluated for all species within 'Campylobacterota'. In order to further expand the knowledge of their phylogenetic relationships and to propose a more robust classification methodology, establishment of clear classification criteria is needed to be evaluated.

In a paper published in the journal PLoS One on 10 December 2020, Taiki Shiotani, Sayaka Mino, Wakana Sato, Sayo Nishikawa, and Masanori Yonezawa of the Laboratory of Microbiology at the Faculty of Fisheries Sciences at Hokkaido University, Stefan Sievert of the Department of Biology at the Woods Hole Oceanographic Institution, and Tomoo Sawabe, also of the Laboratory of Microbiology at the Faculty of Fisheries Sciences at Hokkaido University, report a new thermophilic Campylobacterium, strain EPR55-1T, and evaluate its taxonomic assignment using a comprehensive approach based on whole genome sequence of the phylum 'Campylobacterota'.

The sample of a sulphide chimney structure was collected from the Bio9 deep-sea hydrothermal vent on the East Pacific Rise (9.83˚ N 104.28˚ W, water depth 2511 m) by HOV Alvin during the AT26-23 scientific cruise aboard the R/V Atlantis in 2014. The interior part of the chimney sample was mixed anaerobically with 25 ml sterilised seawater containing 0.05% (w/v) neutralized sodium sulfide in 100 ml glass bottles (Schott Glaswerke) soon after HOV Alvin was recovered.

Cells of EPR55-1T are Gram-negative rods (1.0 ÎĽm long and 0.5 ÎĽm in wide). Cells are motile by means of flagella. Spore formation has not been observed. Strain EPR55-1T grew at temperature between 50˚C and 60˚C, with optimum growth at 60˚C. No growth was observed below 40˚C or above 65˚C. Growth occurred between pH 5.4 and 8.6, with optimum growth at pH 6.6. No growth was detected below pH 3.2 or above pH 9.8. Growth was observed sodium chloride concentrations between 2.4 and 3.2% (weight/volume), with optimum growth at 2.4%. No growth was observed at concentrations below 1.6% or above 4.0%. Temperature, pH, and sodium chloride ranges for growth of strain EPR55-1T were similar to those of 'Nitratiruptor labii' strain HRV44T.

 
Electron micrograph of negatively stained cells of strain EPR55-1T. Scale bar represents 1.0 ÎĽm. Shiotani et al. (2020).

Strain EPR55-1T was only able to use molecular hydrogen as electron donor. Nitrate (0.1%, weight/volume), nitrous oxide (33%, volume/volume), thiosulphate (0.1%, weight/volume), elemental sulfur (1%, weight/volume) and molecular oxygen (0.1%, volume/volume) were able to serve as the sole electron acceptors. The isolate could not utilise any organic compounds as energy or carbon sources. These results indicated that strain EPR55-1T was a strictly hydrogen-oxidizing thermophilic chemolithoautotroph. The isolate was able to use ammonium as its sole nitrogen source and utilisation of molecular nitrogen was not observed. Strain EPR55-1T utilized thiosulphate, sulfite (0.01 to 0.001%, weight/volume) and elemental sulphur as sulphur sources. None of the chemosynthetic 'Campylobacterota' isolated so far are reported as possessing the ability to utilise sulphite as its sulphur source. Strain EPR55-1T was sensitive to ampicillin, chloramphenicol, kanamycin, streptomycin and rifampicin.

With a nearly full length of 16S rRNA gene sequence of strain EPR55-1T as a query in BLAST search, 96.0%, 94.3%, 93.0%, and 93.0% similarity were estimated with 'Nitratiruptor labii' HRV44T, Nitratiruptor sp. SB155-2, Nitratiruptor tergarcus MI55-1T, and Hydrogenimonas thermophila EP1-55-1T, respectively, indicating that strain EPR55-1T may be a new species of Nitratiruptor or even a member of newly described genus with strain HRV44T. The phylogenetic analysis showed that strain EPR55-1T was closely related to the Nitratiruptor species.

 
Phylogenic tree based on 16S rRNA gene sequences. Phylogenetic tree of the members of thermophilic 'Campylobacterota', inferred by the neighbor-joining algorithm using 1,166 homologous sequence positions. Numbers at branches are bootstrap values (%) based on 1,000 replicates. Shiotani et al. (2020).

Hybrid genome assembly with Unicycler resulted in a single complete circular contig with a length of 1 807 889 base pairs. Of the 1833 genes predicted, 1783 were coding sequences, 41 tRNA genes, and 3 set of rRNA genes. These values were comparable to those of closely rerated Nitratiruptor isolates; 'Nitratiruptor labii' HRV44T (1 990 315 base pairs and 2050 coding sequences without a plasmid) Nitratiruptor tergarcus MI55-1T (1 894 691 base pairs and 1935 coding sequences) and Nitratiruptor sp. SB155-2 (1 877 931 base pairs and 1,857 coding sequences). The G + C content was 37.7%, which is similar to that of Nitratiruptor sp. SB155-2 (39.7%). 

 
Maximum likelihood tree of 160 members within 'Campylobacterota'. Maximum likelihood tree was constructed based on amino acid sequences of 139 SCGs using RAxML. Support of internal nodes was calculated using 100 bootstrap iterations. Bootstrap support of 100% and over 75% are denoted by solid and hollow, respectively. Shiotani et al. (2020).

The in silico DNA-DNA hybridisation values of strain EPR55-1T against 'Nitratiruptor labii' HRV44T, Nitratiruptor tergarcus MI55-1T and Hydrogenimonas thermophila EP1-55-1%T were 18.7%, 18.1% and 17.4%, respectively, well below a threshold of 70% in silico DNA-DNA hybridisation used for the definition of Bacterial species. In addition, average nucleotide identity values of strain EPR55-1T against 'Nitratiruptor labii' HRV44T, Nitratiruptor tergarcus MI55-1T and Hydrogenimonas thermophila EP1-55-1%T were 77.5%, 71.4% and 70.4%, respectively, well below the species threshold (95.0%). These results support the proposal that the isolate is a novel species within the class 'Campylobacteria'. Average amino acid identity values of the novel isolate against 'Nitratiruptor labii' HRV44T, Nitratiruptor tergarcus MI55-1T, Nitratiruptor sp. SB155-2 and Hydrogenimonas thermophila EP1-55-1%T were 69.9%, 64.1%, 63.7% and 59.4%, respectively, which fall within the threshold for genus-level differentiation (60–80%). The genome-wide average nucleotide identity and alignment fractions of strain EPR55-1T against the closely related species were 73.85% and 0.53 to 'Nitratiruptor labii' HRV44T, 71.45% and 0.38 to Nitratiruptor tergarcus MI55-1T, 71.32% and 0.38 to Nitratiruptor sp. SB155-2, respectively. These values below the genus level threshold (genome-wide average nucleotide identity value of 73.98 (mean) and 73,11 (median), alignment fraction value of 0.33 (mean) and median (0.345)) are indicative of genus-level differentiation of strain EPR55-1T with strain HRV44T, though percentage of conserved proteins values of strain EPR55-1T against the all three relative strains were over 70.1%, higher than genus threshold (above 50%).

A Venn-diagram showed the presence of a conserved core set of 1270 gene clusters that are shared by all Nitratiruptor genomes, representing more than a half of the proteins in each strain. In addition, strain EPR55-1T, HRV44T, MI55-1T and SB155-2 possessed 215, 345, 250 and 245 singletons, respectively.

 
Venn diagram of orthologous gene clusters among the genera Nitratiruptor and Nitrosophilus. This Venn diagram represents shared or unique orthologous gene clusters between EPR55-1T, HRV44T, Nitratiruptor tergarcus MI55-1T and Nitratiruptor sp. SB155-2. Shiotani et al. (2020).

Average amino acid identity analysis between 160 genomes, which vary extensively within 'Campylobacterota, illustrates that there are genera, which need to be considered reclassification. Average amino acid identity, genome-wide average nucleotide identity, alignment fractions, and percentage of conserved proteins values between type strains of the family Nautiliaceae, Nautilia profundicola AmHT, Caminibacter mediatlanticus TB-2T, Cetia pacifica TB-6T, and Lebetimonas natsushimae HS1857T, were 71.6–74.2%, 76.1–78.0%, 0.52–0.81, and 76.02–84.0%, respectively, within or higher than the genus demarcation given by previous studies. The phylogenomic analyses based on both single-copy core genes and multilocus sequence analysis genes also showed these strains could be regarded as one clade. Although the genome-based taxonomy indicated these strains could be considered to the species belonging the same genus, the current intergenus 16S rRNA gene sequence identities of these strains were below 94.5% with the exception of Cetia pacifica TB-6T which showed more than 95% identity to all type strains of the genus Caminibacter.

 
Consensus neighbour-joining tree of 'Campylobacterota' based on single-copy core genes.The phylogenomic tree was constructed based on 139 SCG protein sequences retrieved from 160 genomes belonging to 'Campylobacterota'. The emended and newly proposed taxa in the phylum 'Campylobacterota' (Nitrosophilus, Caminibacter, Helicobacter I, II, E, F, G, and Arcobacter) are shown in bold. Shiotani et al. (2020).

In addition to the thermophilic taxa, some differences compared to the current classification were observed for the genus Helicobacter and the family Arcobacteraceae. Helicobacter pametensis and Helicobacter cholecystus, Helicobacter brantae showed low average amino acid identity values against other Helicobacter species (48.5–55.8%). Similarly, Helicobacter equorum and Helicobacter himalayensis, and Helicobacter anseris and Helicobacter mustelae showed average amino acid values below the genus threshold against other Helicobacter species (50.0–59.9% and 49.8–55.9%, respectively). Phylogenomic analyses also showed that these six species formed new three clades (Helicobacter E F, and G). Additionally, Helicobacter pylori, Helicobacter acinonychis, and Helicobacter cetorum, currently belonging to the Helicobacter clade, showed lower average amino acid identity values than the genus threshold against other current Helicobacter clade species (57.0–58.1%). In the both neighbour-joining and maximum likelihood phylogenomic trees on the basis on 139 single-copy core genes, the current Helicobacter clade branched to two clades (Helicobacter I and II). Same branching patterns were also observed in the neighbour-joining tree based on amino acid sequences of multilocus sequence analysis genes. In the genera of the family Arcobacteraceae, average amino acid identity values between species belonging to different genera Aliarcobacter, Poseidonibacter, Malaciobacter, Arcobacter, Halarcobacter were 61.9–78.7%, indicating they could be regarded as different species of the same genus. The large clade consisting of these genera was also identified by phylogenomic analyses based on both single-copy core genes and multilocus sequence analysis genes. However, some species showed the inter-genus 16S rRNA gene sequence identities below 94.5%, indicating differentiation at genus level. Average amino acid identity values among Campylobacter B were relatively lower (57.02–65.86%), possibly due to the low degree of relatedness between Campylobacter B species (less than 94.5% 16S rRNA gene similarities).

 
Consensus neighbour-joining tree of 'Campylobacterota' based on multilocus sequence analysis genes. The phylogenetic tree was constructed based on amino acid sequences of multilocus sequence analysis genes (i.e. atpA, dnaK, glyA, gyrB, metG, pheS and tkt) retrieved from 154 members of 'Campylobacterota'. Arcobacter cloacae F26, Arcobacter ebronensis CECT 8441, Arcobacter mediterraneus F156-34, Campylobacter mucosalis DSM 21682, Helicobacter bizzozeronii CIII-1, Hydrogenmonas sp. MAG80, and Thiovulum sp. ES were excluded because of lack of at least one multilocus sequence analysis gene sequence. Shiotani et al. (2020).

Based on results of phylogenomic analyses, the average amino acid identity values between species belonging to same clades or the different clades were evaluated. The minimum average amino acid value between species belonging to same clades was 59.7% (Helicobacter muridarum ST1T vs Helicobacter saguini MIT 97-6194T), and the maximum average amino acid identity value between species belonging to different clades was 61.9% (Campylobacter geochelonis RC20T vs Campylobacter hominis ATCC BAA-381T) with the exception of Nitratiruptoraceae, Nautiliaceae, and Arcobacteraceae whose 16S rRNA gene sequence similarities were not reflected in the genome relatedness. These values indicated the average amino acid identity threshold for genus demarcation of 'Campylobacterota' was about 60–62%, though there are some exceptions.

Strain EPR55-1T was the first Nitratiruptoraceae species isolated from the East Pacific Rise. The strain shows some physiological differences from other Nitratiruptoraceae isolates, and represents the only Nitratiruptoraceae species which is able to utilise thiosulphate and sulphite as its sole electron acceptor and sulfur source, respectively. The ability to utilise sulphite has also never been reported in any other thermophilic Campylobacterial species. The strain EPR55-1T possessed lophotrichous flagella, unlike the monotrichous and amphitrichous flagella of 'Nitratiruptor labii' and Nitratiruptor tergarcus, respectively. 16S rRNA gene sequence similarities,genome-wide average nucleotide identity and alignment fraction values of the strain against closely related species suggested that strain EPR55-1T designate the strain as a novel genus with strain HRV44T. The strain EPR55-1T therefore represents a novel genus within a new genus of the family Nitratiruptoraceae.

Strain EPR55-1T is therefore described as a new species, Nitrosophilus alvini, where 'Nitrosophilus' derives from 'nitrosus', full of natron, intended to mean nitrate and nitrous oxide, and 'philos', loving, friendly to, and 'alvini' derives from the name of the HOV Alvin which collected the deep-sea hydrothermal samples harbouring this strain). 

Cells are rod-shaped, motile and stain Gram-negative. Anaerobic to microaerobic. Strictly chemolithoautotrophic. Thermophilic, adapted to the salinity of the ocean. On the basis of 16S rRNA gene and single-copy core-gene analyses, the genus Nitrosophilus belongs to the family Nitratiruptoraceae within the class 'Campylobacteria'.

The temperature range for growth is at 50– 60˚C (optimum 60˚C). The pH range for growth is pH 5.4–8.6 (optimum 6.6). Sodium Chloride concentration range for growth is 2.4–3.2% (weight/volume) (optimum 2.4%). Strain EPR55-1T is hydrogen-oxidising, facultatively anaerobic and chemolithoautotrophic with molecular hydrogen as its sole electron donor and with nitrate, nitrous oxide, thiosulfate, molecular oxygen or elemental sulphur as its sole electron acceptors. Ammonium is utilised as its sole nitrogen source. Thiosulphate, sulphite or elemental sulphur are utilised as its sole sulphur source. The complete genome size is 1 807 889 base pairs. The guanine + cytosine content of DNA is 37.7%. The type strain, EPR55-1T (otherwise known as JCM 32893T and KCTC 15925T), was isolated from a deep-sea hydrothermal vent in the East Pacific Rise.

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Friday, 1 January 2021

Monitoring the recovery of hydrothermal vent communities after volcanic eruptions.

Deep-sea hydrothermal vents host intriguing communities that are fuelled by chemosynthesis and occur on active seafloor geological features such as mid-ocean ridges, back-arc basins, and seamounts. The habitat in these settings is patchy and subject to catastrophic eruptive disturbance, so the persistence of vent species depends on their ability, predominantly as larvae, to disperse and colonise other vents. In order tounderstandthe resilience of this system, it is important to quantify how quickly vent communities recover from disturbance,what processes influence their ability to recover, and how processes at an individual vent field affect community dynamics, persistence, and species diversity on the regional scale.

The ability of a species to disperse successfully from one vent patch to another depends on factors including the spatial separation of the vents, larval dispersal capabilities, and habitat requirements of new colonists. Vents occur in patterns aligned with locations of magma intrusion into the ocean crust at plate boundaries, often along topographic features such asmid-ocean ridges, volcanic arcs, and backarc spreading centres. In regions with relatively high magma supply rate, such as the East Pacific Rise, vent fields are separated by a few to tens of kilometres, whereas in areas with slower spreading rates, such as the Mid-Atlantic Ridge and some back-arc spreading systems, vent fields may be separated by hundreds of kilometres. Larvae are transported in ocean currents, and must locate suitable physical and chemical habitat within a vent field to colonise successfully. Vent fluid chemistry varies across individual vent orifices and over time. Species differ in their vent habitat requirements, so colonisation of any one species depends not only on its ability to reach a new vent but on the habitat characteristics it encounters there. Even if larvae colonize successfully, a population may fail to persist as the local conditions change, or as it interacts with other species during succession.

Disturbances at vent-field scale that eradicate the local community occur mainly through volcanic eruptions or landslides. The frequency of disturbance may range from almost continuous at vents on submarine arc volcanoes with multiyear eruptions (e.g. NW Rota-1, a seamount in the Mariana Islands, northwest of Rota Island) to very infrequent at vents on slow-spreading ridges. At spreading ridges, the frequency of volcanic eruptions (like the spacing of vents) is related to magma supply: at the fast-spreading East Pacific Rise, vent communities are eradicated by seafloor eruptions on decadal timescales, whereas at the slow-spreading Mid-Atlantic Ridge an eruption might not occur for 10 000 years. These natural eruptive disturbances appear to be a fundamental regulating feature of vent populations and communities at volcanically active areas, as both the disturbance frequency and vent spacing are expected to influence connectivity among vents.

A fundamental question in vent ecology is the resilience of communities to disturbance, including the recovery time in an individual vent field, and the regional persistence of groups of communities (metacommunities) connected across fields by dispersal. Efforts to investigate recovery of vent communities, by monitoring colonisation and species assembly, have taken advantage of local extinctions driven by seafloor volcanic eruptions at vents on the East Pacific Rise and Juan de Fuca Ridge. These field studies, all conducted in frequently disturbed systems, have been interpreted to suggest that typical vent community recovery times may be as short as 2–4 years, and are characteristic of a resilient fauna adapted to disturbance events. The caveats on those estimates, and assumptions underlying the interpretations, need to be examined critically. Identifying a pre-disturbance baseline can be difficult, and the time to re-establish a disturbed state may be much shorter than to establish a climax community, especially if the regional diversity is high. Furthermore, recovery of vent communities in other regions exposed to much lower frequencies of catastrophic disturbance, such as the Mid-Atlantic Ridge or some regions of the western Pacific, may be slower. Communities in those regions appear to be relatively stable over periods of years to decades, in the absence of disturbance on a vent-field scale. Understanding the processes contributing to recovery of both community structure and function is essential for interpreting these field results and using them to predict resilience more generally across a spectrum of disturbance regimes.

Renewed interest in extracting resources from deep-sea mineral deposits has led to an urgent need for a better understanding of vent community recovery and metacommunity resilience. The prospect of seafloor mining of sulphide deposits puts vent communities at risk in some of the areas where connectivity and resilience are least well known. The first demonstration of sulphide mining at a deep-sea vent occurred in the Okinawa Trough in 2017. As of 2019, eight nations had polymetalic sulphide mining exploration contracts under the International Seabed Authority, and another eight had allowed mining research or exploration at vents in waters of their national jurisdiction.

In a paper published in the journal Proceedings of the Royal Society Series B: Biological Sciences on 23 December 2020, Lauren Mullineaux, and Susan Mills of the Biology Department at the Woods Hole Oceanographic Institution, Nadine Le Bris of the Benthic Ecogeochemistry Laboratory at Sorbonne Université and Stace Beaulieu, Stefan Sievert, and Lauren Dykman, also of the Biology Department at the Woods Hole Oceanographic Institution, present the results of a study which aimed to investigate the rate and nature of ecological succession after a catastrophic disturbance.

 
Conceptual framework for community recovery in frequently disturbed deep-sea hydrothermal vent systems. Increase in number of species following frequent disturbance events (thin curves), does not reach potential species number in a community subject to less frequent disturbance (thick curve). Pre-eruption species number is not a consistent baseline because it depends on the time since prior disturbance. Mullineaux et al. (2020).

Mullineaux et al. took advantage of a massive seafloor eruption in 2006 on the East Pacific Rise where we were able to initiate post-eruption observations within months and continue them uninterrupted for more than a decade, providing an extensive colonisation time series that is unprecedented for the deep sea. These data enable a critical evaluation of recovery time in a frequently disturbed vent system, and its relevance to a broader spectrum of disturbance regimes. The vent system represents an intriguing case for succession, where both connectivity and disturbance are closely tied to earth dynamics, and informs broader efforts to understand and predict changes in community structure in response to natural and human disturbance.

Experiments and habitat characterization for this study were conducted on the East Pacific Rise, on a series of cruises starting five months after a catastrophic eruption in January 2006 that eradicated the communities in a vent field located along the ridge between 9°48' and 9°52'. Vent communities at 9°47' North and further south persisted. A prior eruption in 1991 had also eradicated communities in this part of this ridge segment. Mullineaux et al. had been monitoring larval supply and colonization at these vents in the years between the two eruptions, and participated in a rapid-response cruise directly after the 2006 event. In the 11 years since, Mullineaux et al. have accumulated a near-continuous record of colonisation at sites at 9°50' North and neighbouring vents, in some cases with associated measurements of larval supply and/or vent fluid composition.

 
Experimental design and biologically relevant chemical characteristics at P-vent near 9°50’ North on the East Pacific Rise. (a) Schedule of deployment and recovery of colonization sandwiches on research vessels Atlantis (AT designates cruise number) and L’Atalante, in months after the 2006 eruption (those recovered on the L’Atalante cruise were unusable due to ferrous precipitate; inset shows colonised sandwich in Alvin manipulator; (b) change in temperature over months post-eruption; (c) relationship of pH with temperature; (d) relationship of total sulfide with temperature. Mullineaux et al.

Colonisation monitoring was focused at a diffuse-flow vent site near P-vent (9.838° North, 104.291°West, 2509 m depth) where venting continued through the duration of the study. Colonisation surfaces were deployed and recovered using the Human-occupied submersibles Alvin and Nautile, and the remotely operated vehicle Jason, with recoveries occurring at time points of 9, 11, 22, 33, 96, 106, and 135 months after the eruption. A few early (nine months) samples were included from a transient vent near the Ty/Io vent, 200 m south of P-vent, but that site was abandoned when it became clear that venting had waned precipitously after the first cruise.

 
Location of the East Pacific Rise vent sites between 9°410' and 9°510' North. Georgieva et al. (2014).

Colonists (larvae that had settled) were collected on experimental surfaces, termed ’sandwiches’, comprising six layered 10 × 10 cm Lexan plastic plates, each 0.7 cm thick and separated from each other by 1 cm to provide roughly 12 000 cm² surface area. For each deployment, replicate sandwiches were placed in each of three distinct habitat types, characterised by temperature as hot (7–30°C), warm (3–7°C), or cool (2–3°C). These habitat types correspond to the faunal zones listed by Fiorenza Micheli, Charles Peterson, Lauren Mullineaux, Charles Fisher, Susan Mills, Gorka Sancho, Galen Johnson, and Hunter Lenihan, in a paper published in 2002, as Vestimentiferan (Tubeworm), Bivalve, and suspension-feeder, respectively. Habitat temperature was measured at the base of each sandwich, on deployment and recovery, with a temperature probe for 1–2 min until a clear maximum value was observed. The maximum value of the recovery temperature was used to characterize the thermal environment of the surface, for consistency with prior studies. These temperature measurements are useful for characterising the general thermal habitat of a sandwich, even though the specific temperature experienced by an individual colonist could vary over the extent of the surface and over tidal and shorter timescales. Due to logistical limitations, not all habitats were sampled for each interval. In many cases, the thermal habitat changed over the course of a deployment, as temperatures overall tended to decrease with time. To account for this variation, both the deployment zone and the recovery temperature were taken into account when interpreting colonisation results. 

On recovery, each sandwich was placed in an individual collection compartment for transport back to the ship and subsequent analysis of colonists. On board, sandwiches and their attached colonists were preserved in 80% ethanol, as were any individuals that had become detached in the compartment and were retained on a 63 ÎĽm sieve. In the laboratory, each surface was examined under a dissecting microscope and all metazoan colonists (including detached individuals greater than 1 mm) were enumerated and identified to species or the lowest taxonomic group possible. Meiofauna that were too small or mobile to be retained reliably in the samples, or outside our taxonomic expertise, were not included in the analyses.

Species or morphogroup abundance was assessed for each recovery date on three replicate sandwiches from each available habitat. Abundance of a subset of species, selected based on their demonstrated role in prior succession studies and/or prominence in the current samples, was compared across time with a non-parametric Kruskal–Wallace test (a non-parametric method for testing whether samples originate from the same distribution). Analyses of the full community species composition were conducted with nonmetric multidimensional scaling to visualize the change in composition over time. Relative abundance (compared to total number of individuals in the sample) was used in the nonmetric multidimensional scaling to compensate for different deployment intervals or surface types, and log transformed to avoid dominance of pattern by abundant species. Numbers of colonists varied widely between samples, so diversity was assessed by a rarefaction analysis, with total individuals pooled over replicates. Single-celled Protozoans were not included in nonmetric multidimensional scaling or rarefaction analyses, as their occasional outlier abundances obscured patterns displayed by the Metazoans.

Colonisation data from prior to the eruption were available from several vents located within a few hundred metres of the P-vent site, and were selected from the East Wall vent collections to represent a range of thermal habitats similar to P-vent, an extended deployment time (37 months), and the most mature successional stage available (85 months after the previous eruption in 1991). These pre-eruption colonisation experiments had been conducted on basalt blocks with similar collecting characteristics but smaller surface area than the sandwiches, so comparisons with post-eruption results were made on relative abundance.

Free sulphide (i.e. sulphide and hydrogen sulphide ions and dihydrogen sulphide molecules), pH, and temperature were measured in close vicinity to colonisers at 11, 24, 33, and 96 months after the 2006 eruption as in. Mullineaux et al. used a silver sulphide electrode (0.8 mm diameter) associated with a miniaturised glass electrode (1.5 mm) connected to individual potentiometric loggers at 11, 22, and 33 months. A 0.1 mm disc mercury amalgam electrode connected to an underwater potentiostat was used to measure free sulphide by cyclic voltammetry at month 96. The electrodes were combined with a temperature probe (3 mm diameter). Precise positioning and stabilisation of the tip using the submersible arm allowed continuous data records of 1 to 3 min on each location (at the frequency of 4–12 measurements per minute for potentiometry and one triplicate measurement per minute for voltammetry). Average values defined for each measurement sequence integrate fluctuations and allow characterising chemical gradients as a function of temperature with a spatial resolution much finer than the sandwich size.

Abiotic conditions around sandwiches at P-vent after the eruption show a typical increase of free sulphide and decrease of pH with temperature consistent with mixing of local diffuse vent fluids with ambient seawater being the primary driver of habitat abiotic ranges. When compared with the first time point (12 months post-eruption), the narrower ranges of sulphide, pH, and temperature at 24, 33, and 96 months indicate habitat conditions with lower vent fluid contribution, depleted in sulphide and less acidic. Temperatures recorded at 24 and 33 months were typically low because vent fluid flux had decreased at the location of sandwich deployments. Temperatures at 96 months were higher because monitoring had moved to areas with more vigorous venting.

Colonisation of prominent species varied across the series of deployments, showing a distinct progression over time. The Limpet Ctenopelta porifera appeared only in the first 22 months, and primarily in hot habitat. This species may have failed to persist because its preferred high-temperature habitat (typically greater than 15°C; electronic supplementary material) lasted only 2 to 3 years after the eruption. Its arrival is of particular interest because it was a pioneer from afar and had not been reported within 350 km of this site prior to the 2006 eruption. Siboglinid (Vestimentiferan) Tubeworms, including individuals identified as Riftia pachyptila and Tevnia jerichonana, and other individuals too small to identify to species, arrived predominantly in the first 33 months post-eruption, mostly in hot or warm habitat. They were represented by a few individuals in the 96, 106, and 135 month samples, including some in cool habitat. The Limpet Lepetodrilus tevnianus also colonised mostly in hot and warm habitat and declined after 33 months. The Vent Mussel Bathymodiolus thermophilus occurred in all habitat types, became abundant at 22 and 33 months after the eruption, and persisted through 135 months. The Limpet Gorgoleptis spiralis showed a similar temporal pattern, but was found in hot habitat only at 106 months. The small, tube-building Polychaete species Laminatubus alvini arrived at 22 months, persisted through 135 months, and occurred in all habitats. The Protozoans Abyssotherma pacifica (a chambered Foraminiferan), and Metafolliculina sp. (a tube-dwelling Ciliate) also occurred at 22 months and beyond in all habitats.

 
Abundance (log-transformed) of prominent species colonising sandwiches at P-vent after the 2006 eruption. Values are mean of replicates (usually 3) deployed in hot, warm, and cool habitat. Bars are standard error; ‘nd’ indicates no sandwiches recovered. Mullineaux et al. (2020).

A distinct, directional trend in community composition was evident over the months following the 2006 eruption. In each of the hot, warm, and cool habitats, composition of the post-eruption samples became progressively more similar to pre-eruption samples during the first 96 months. Later in the series, however, composition bypassed or deviated from the pre-eruption state. Although the pre-eruption samples were intended to represent a ’baseline’ community, it is important to remember that they had been collected only 85 months after the previous eruption in 1991. The observed changes in post-eruption composition were directional along one dimension (horizontal axis), but not the other. In some cases, the differences between replicate samples at one recovery date were equal to, or greater than, differences between dates. Both of these patterns indicate that factors other than time influence composition, and microhabitat variation is a likely candidate, as recovery temperatures of the sandwiches varied across replicates.

 
Species composition and diversity of colonists at P-vent after the 2006 eruption. Nonmetric multidimensional scaling analyses in hot (a), warm (b), and cool (c) habitat (stress = 0.06, 0.09, 0.10, respectively, where less than 0.05 indicates good fit; proportion of variance = 0.98, 0.96, and 0.94). P-vent samples (blue) are labelled by temperature (°C) and shaded by months post-eruption; pre-eruption samples (orange) provided for comparison. Species assembly (rarefaction) curves in hot (d), warm (e), and cool (f) habitat; data for each recovery date are pooled from replicate samples (usually 3). Mullineaux et al. (2020).

Species richness of post-eruption colonists, as measured by rarefaction, generally increased over time For many recovery dates, sample sizes were too low to reach an accurate assessment of full richness (as displayed by lack of asymptote in the curve), but the species number at a given sample size allows for comparison across dates. In the hot habitat, post-eruption richness increased from 9 to 33 months after the eruption, and at 106 months exceeded the pre-eruption level. By contrast, in the warm and cool habitat, post-eruption richness reached or exceeded the pre-eruption level by 22 months.

A compilation of vent species reported from the area near 9° North East Pacific Rise can be added to Mullineaux et al.'s observations to identify the potential species pool for recolonisation of disturbed vents. Filtering this list so it includes only taxa that could be sampled with sandwiches results in a total of 91 taxa. Of these, 67 were observed in the post-eruption samples overall, but only 29 were in the 135-month samples, representing 74% and 32% of the regional species pool, respectively.

More than a decade after an eruption destroyed vent communities on the East Pacific Rise, the species composition of new colonists appeared to still be changing and the successional stage appeared to be different than in the prior, pre-eruption, community. These results suggest that important successional processes continue well beyond the 3–4 years that have previously been monitored after a seafloor disturbance event, and that prior estimates of recovery time need to be re-evaluated.

Temporal changes in environmental conditions clearly influenced succession in this system, especially early in the sequence. In the months directly following the eruption, rapid changes occurred in vent fluid flow distribution, resulting in closure of some newly opened vents, and rapid changes in thermal and chemical habitat, as observed at P-vent. Mullineaux et al. suspect that the rapid decrease of the Gastropod Ctenopelta porifera and other species during this stage may have been driven by loss of the unique habitat created by the unusually vigorous venting of sulphide-rich fluids directly from basalt orifices. Within 20 months past the eruption, maximal temperatures in the hot zone had dropped from 30°C to below 15°C, and sulphide concentration had declined substantially compared to the post-eruption maximum. However, spatial variation in environmental conditions across the hot, warm, and cool zones persisted, and supported different faunas across those zones. This environmental variation across the vent landscape creates a mosaic of habitat types, with variable chemical resource supply and abiotic constraints, which needs to be considered when characterising succession and quantifying recovery.

After two years into the successional sequence, new species continued to arrive (10 total), even though the temperatures had stabilized to a range of 2–10°C across the habitats, andto 2.0–4.2°C directly at the sandwiches.Other species disappeared as colonists (11 total), although they may have persisted in the surrounding community as adults. In these later years, it is likely that differences in species’ life-history traits, such as reproduction and larval dispersal, and species interactions become more important in driving patterns such as the gradual increase in species richness. These types of biological processes can be detected only through long-term monitoring and sampling across environmental zones.

Evaluating community recovery typically involves a comparison of species diversity or composition to a predisturbance, or undisturbed, ’baseline’. If Mullineaux et al. adopt this approach, using the pre-eruption species richness as baseline, then they would conclude from rarefaction curves that P-vent was approaching recovery as early as 2 years after the eruption in the warm and cool habitats. In our observations, the diversity even surpassed the pre-eruption state after roughly 3 years. If Mullineaux et al. use species composition instead (occurrence and relative abundance in nonmetric multidimensional scaling plots), then they conclude that the community was approaching recovery to baselinewithin 8–9 years after the eruption. However, the species composition was still changing at 11 years, and was dissimilar to the pre-eruption state, indicating that the communities may have bypassed the preeruption communities along the successional sequence, and may continue to change. The pre-eruption observations likely did not represent an equilibrium or climax community, as they were from samples collected 7 years after the previous eruption in 1991. This comparison illustrates the challenge in selecting and evaluating a pre-disturbance baseline community. An alternative approach to quantify recovery is to compare community composition during succession to regional species pools. Using the species list developed by Damien Desbruyères, Michel Segonzac and Monica Bright for for 9° North East Pacific Rise, Mullineaux et al. found only 42% of the regional species pool in our pre-eruption samples, 73% across all of the post-eruption samples, and only 32% at the final 11-year date, suggesting that further changes over time may occur.

Prior studies of vent community recovery provide examples of how undersampling the diversity of habitat type or the species in a baseline community can lead to an underestimate of recovery time at a disturbed site. At Juan de Fuca Ridge, Verena Tunnicliffe, Robert Embley, James Holden, David Butterfield, Gary Massoth, and Kim Juniper, reported that 16 species out of a baseline pool of 30 (53%) had re-established within 2 years of an eruption, plus an additional 10 species not in the baseline. The baseline had been documented at one time point from a single, nearby, undisturbed vent with limited habitat diversity, and so did not represent the full diversity of potential source colonists in the area, leading to an underestimate of recovery time. On the East Pacific Rise after the 1991 eruption near 9° N, Timothy Shank, Daniel Fornari, Karen Von Damm, Marvin Lilley, Rachel Haymon, and Richard Lutz, observed 32 species out of a baseline pool of 45 (71%) had returned by 4.5 years after the disturbance but faunal lists did not include many small species that are typical of vent communities at the  East Pacific Rise. Small species tend to arrive later in vent successional sequences, so a sampling method that misses them will likely result in a faster estimate of recovery time.

Interpretation of field observations of vent community recovery from disturbance differs substantially depending on whether the focus is on re-assembly of species at a single vent field, or on the persistence of species diversity across sites in a region (i.e. across the metacommunity). From the single-site perspective, the question is simply how quickly the pre-disturbance community becomes established, and it does not matter whether the pre-eruption state had low species diversity due to recent prior disturbance or to low habitat diversity. From a metacommunity perspective, it becomes important to know whether a sufficient number of communities, occupying a spectrum of habitat diversity, recover from disturbance far enough through the successional stages to support regional species diversity. If disturbance becomes too frequent, or spatially extensive, to support a mosaic of communities representing the full spectrum of successional stages, then diversity of the regional species pool will decline. This more complicated perspective requires sampling at multiple sites, but is critical for understanding the dynamics and distributions of vent species.

Such an understanding is precisely what policymakers are calling for in order to anticipate and manage the impacts of mining of vent deposits and other seafloor resources. Mullineaux et al.'s observations of prolonged recovery time at a frequently disturbed vent site, previously expected to recover particularly rapidly, caution that vent communities, in general, may be less resilient to mining disturbance than originally expected. This reinforces the importance of assessing community recovery against baselines that account for regional factors such as habitat spacing, connectivity, and regional species pools. Mining will take place over expansive areas for prolonged periods of time, which poses particular risk to species with low colonisation rates when many adjacent sites are destroyed. Importantly, an understanding of frequently disturbed vent communities in the eastern Pacific, even from the metacommunity perspective, cannot be extrapolated to predict recovery from mining of seafloor sulphides elsewhere in the world’s oceans. This study nevertheless suggests that multiple factors can influence the dynamics of reestablishing communities in naturally unstable systems. This is particularly critical as species diversity has been described only for a few vent sites, and we know even less about the diversity of habitat types and their temporal stability, particularly on complex arc and back-arc systems. Furthermore, sites of particular interest for exploitation include large sulphide deposits that appear to have been active for thousands of years, and may be located far from other potential source communities, leading to very different recovery dynamics.

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