Pachiadaki Maria G.

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Pachiadaki

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Maria G.

ORCID

0000-0003-2684-7501

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Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples

( 2014-10) Edgcomb, Virginia P. ; Taylor, Craig D. ; Pachiadaki, Maria G. ; Honjo, Susumu ; Engstrom, Ivory B. ; Yakimov, Michail M.

Obtaining an accurate picture of microbial processes occurring in situ is essential for our understanding of marine biogeochemical cycles of global importance. Water samples are typically collected at depth and returned to the sea surface for processing and downstream experiments. Metatranscriptome analysis is one powerful approach for investigating metabolic activities of microorganisms in their habitat and which can be informative for determining responses of microbiota to disturbances such as the Deepwater Horizon oil spill. For studies of microbial processes occurring in the deep sea, however, sample handling, pressure, and other changes during sample recovery can subject microorganisms to physiological changes that alter the expression profile of labile messenger RNA. Here we report a comparison of gene expression profiles for whole microbial communities in a bathypelagic water column sample collected in the Eastern Mediterranean Sea using Niskin bottle sample collection and a new water column sampler for studies of marine microbial ecology, the Microbial Sampler – In Situ Incubation Device (MS-SID). For some taxa, gene expression profiles from samples collected and preserved 33 in situ were significantly different from potentially more stressful Niskin sampling and 34 preservation on deck. Some categories of transcribed genes also appear to be affected by sample 35 handling more than others. This suggests that for future studies of marine microbial ecology, 36 particularly targeting deep sea samples, an in situ sample collection and preservation approach 37 should be considered.
Protist community grazing on prokaryotic prey in deep ocean water masses

(Public Library of Science, 2015-04-20) Rocke, Emma ; Pachiadaki, Maria G. ; Cobban, Alec ; Kujawinski, Elizabeth B. ; Edgcomb, Virginia P.

Oceanic protist grazing at mesopelagic and bathypelagic depths, and their subsequent effects on trophic links between eukaryotes and prokaryotes, are not well constrained. Recent studies show evidence of higher than expected grazing activity by protists down to mesopelagic depths. This study provides the first exploration of protist grazing in the bathypelagic North Atlantic Deep Water (NADW). Grazing was measured throughout the water column at three stations in the South Atlantic using fluorescently-labeled prey analogues. Grazing in the deep Antarctic Intermediate water (AAIW) and NADW at all three stations removed 3.79% ± 1.72% to 31.14% ± 8.24% of the standing prokaryote stock. These results imply that protist grazing may be a significant source of labile organic carbon at certain meso- and bathypelagic depths.
Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system

(Frontiers Media, 2019-06-12) Labonté, Jessica M. ; Pachiadaki, Maria G. ; Fergusson, Elizabeth ; McNichol, Jesse C. ; Grosche, Ashley ; Gulmann, Lara K. ; Vetriani, Costantino ; Sievert, Stefan M. ; Stepanauskas, Ramunas

Phage–host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host’s protection against toxic metals and antibacterial compounds.
Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters

(Frontiers Media, 2022-01-06) Suter, Elizabeth A. ; Pachiadaki, Maria G. ; Taylor, Gordon T. ; Edgcomb, Virginia P.

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.
Anomalous delta C-13 in particulate organic carbon at the chemoautotrophy maximum in the Cariaco Basin

(Journal of Geophysical Research-Biogeosciences, 2020-01-30) Scranton, Mary I. ; Taylor, Gordon T. ; Thunell, Robert C. ; Muller-Karger, Frank E. ; Astor, Yrene ; Swart, Peter K. ; Edgcomb, Virginia P. ; Pachiadaki, Maria G.

A chemoautotrophy maximum is present in many anoxic basins at the sulfidic layer's upper boundary, but the factors controlling this feature are poorly understood. In 13 of 31 cruises to the Cariaco Basin, particulate organic carbon (POC) was enriched in 13C (δ13CPOC as high as −16‰) within the oxic/sulfidic transition compared to photic zone values (−23 to −26‰). During “heavy” cruises, fluxes of O2 and [NO3− + NO2−] to the oxic/sulfidic interface were significantly lower than during “light” cruises. Cruises with isotopically heavy POC were more common between 2013 and 2015 when suspended particles below the photic zone tended to be nitrogen rich compared to later cruises. Within the chemoautotrophic layer, nitrogen‐rich particles (molar ratio C/N< 10) were more likely to be 13C‐enriched than nitrogen‐poor particles, implying that these inventories were dominated by living cells and fresh detritus rather than laterally transported or extensively decomposed detritus. During heavy cruises, 13C enrichments persisted to 1,300 m, providing the first evidence of downward transport of chemoautotrophically produced POC. Dissolved inorganic carbon assimilation during heavy cruises (n = 3) was faster and occurred deeper than during light cruises (n = 2). Metagenomics data from the chemoautotrophic layer during two cruises support prevalence of microorganisms carrying RuBisCO form II genes, which encode a carbon fixation enzyme that discriminates less against heavy isotopes than most other carbon fixation enzymes, and metatranscriptomics data indicate that higher expression of form II RuBisCO genes during the heavy cruises at depths where essential reactants coexist are responsible for the isotopically heavier POC.
Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia.

(Frontiers Media, 2019-03-22) Torres-Beltrán, Mónica ; Mueller, Andreas ; Scofield, Melanie ; Pachiadaki, Maria G. ; Taylor, Craig D. ; Tyshchenko, Kateryna ; Michiels, Céline ; Lam, Phyllis ; Ulloa, Osvaldo ; Jürgens, Klaus ; Hyun, Jung-Ho ; Edgcomb, Virginia P. ; Crowe, Sean A. ; Hallam, Steven J.

The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 Microbial Community Responses to Ocean Deoxygenation workshop held in Vancouver, B.C on July 2014 had the primary objective of initiating a process to standardize operating procedures for compatible process rate and multi-omic (DNA, RNA, protein, and metabolite) data collection in marine oxygen minimum zones and other oxygen depleted waters. Workshop attendees participated in practical sampling and experimental activities in Saanich Inlet, British Columbia, a seasonally anoxic fjord. Experiments were designed to compare and cross-calibrate in situ versus bottle sampling methods to determine effects on microbial community structure and potential activity when using different filter combinations, filtration methods, and sample volumes. Resulting biomass was preserved for small subunit ribosomal RNA (SSU or 16S rRNA) and SSU rRNA gene (rDNA) amplicon sequencing followed by downstream statistical and visual analyses. Results from these analyses showed that significant community shifts occurred between in situ versus on ship processed samples. For example, Bacteroidetes, Alphaproteobacteria, and Opisthokonta associated with on-ship filtration onto 0.4 μm filters increased fivefold compared to on-ship in-line 0.22 μm filters or 0.4 μm filters processed and preserved in situ. In contrast, Planctomycetes associated with 0.4 μm in situ filters increased fivefold compared to on-ship filtration onto 0.4 μm filters and on-ship in-line 0.22 μm filters. In addition, candidate divisions and Chloroflexi were primarily recovered when filtered onto 0.4 μm filters in situ. Results based on rRNA:rDNA ratios for microbial indicator groups revealed previously unrecognized roles of candidate divisions, Desulfarculales, and Desulfuromandales in sulfur cycling, carbon fixation and fermentation within anoxic basin waters. Taken together, filter size and in situ versus on-ship filtration had the largest impact on recovery of microbial groups with the potential to influence downstream metabolic reconstruction and process rate measurements. These observations highlight the need for establishing standardized and reproducible techniques that facilitate cross-scale comparisons and more accurately assess in situ activities of microbial communities.
A review of protist grazing below the photic zone emphasizing studies of oxygen-depleted water columns and recent applications of in situ approaches

(Frontiers Media, 2017-04-26) Medina Faull, Luis E. ; Taylor, Craig D. ; Pachiadaki, Maria G. ; Henríquez-Castillo, Carlos ; Ulloa, Osvaldo ; Edgcomb, Virginia P.

Little is still known of the impacts of protist grazing on bacterioplankton communities in the dark ocean. Furthermore, the accuracy of assessments of in situ microbial activities, including protist grazing, can be affected by sampling artifacts introduced during sample retrieval and downstream manipulations. Potential artifacts may be increased when working with deep-sea samples or samples from chemically unique water columns such as oxygen minimum zones (OMZs). OMZs are oxygen-depleted regions in the ocean, where oxygen concentrations can drop to <20 μM. These regions are typically located near eastern boundary upwelling systems and currently occur in waters occupying below about 8% of total ocean surface area, representing ~1% of the ocean's volume. OMZs have a profound impact not only on the distribution of marine Metazoa, but also on the composition and activities of microbial communities at the base of marine food webs. Here we present an overview of current knowledge of protist phagotrophy below the photic zone, emphasizing studies of oxygen-depleted waters and presenting results of the first attempt to implement new technology for conducting these incubation studies completely in situ (the Microbial Sampling- Submersible Incubation Device, MS-SID). We performed 24-h incubation experiments in the Eastern Tropical South Pacific (ETSP) OMZ. This preliminary study shows that up to 28% of bacterial biomass may be consumed by protists in waters where oxygen concentrations were down to ~4.8 μM and up to 13% at a station with nitrite accumulation where oxygen concentrations were undetectable. Results also show that shipboard measurements of grazing rates were lower than rates measured from the same water using the MS-SID, suggesting that in situ experiments help to minimize artifacts that may be introduced when conducting incubation studies using waters collected from below the photic zone, particularly from oxygen-depleted regions of the water column.
The Deep Ocean Observing Strategy: addressing global challenges in the deep sea through collaboration

(Marine Technology Society, 2022-06-08) Smith, Leslie M. ; Cimoli, Laura ; LaScala-Gruenewald, Diana ; Pachiadaki, Maria G. ; Phillips, Brennan T. ; Pillar, Helen R. ; Stopa, Justin ; Baumann-Pickering, Simone ; Beaulieu, Stace E. ; Bell, Katherine L. C. ; Harden-Davies, Harriet ; Gjerde, Kristina M. ; Heimbach, Patrick ; Howe, Bruce M. ; Janssen, Felix ; Levin, Lisa A. ; Ruhl, Henry A. ; Soule, S. Adam ; Stocks, Karen ; Vardaro, Michael F. ; Wright, Dawn J.

The Deep Ocean Observing Strategy (DOOS) is an international, community-driven initiative that facilitates collaboration across disciplines and fields, elevates a diverse cohort of early career researchers into future leaders, and connects scientific advancements to societal needs. DOOS represents a global network of deep-ocean observing, mapping, and modeling experts, focusing community efforts in the support of strong science, policy, and planning for sustainable oceans. Its initiatives work to propose deep-sea Essential Ocean Variables; assess technology development; develop shared best practices, standards, and cross-calibration procedures; and transfer knowledge to policy makers and deep-ocean stakeholders. Several of these efforts align with the vision of the UN Ocean Decade to generate the science we need to create the deep ocean we want. DOOS works toward (1) a healthy and resilient deep ocean by informing science-based conservation actions, including optimizing data delivery, creating habitat and ecological maps of critical areas, and developing regional demonstration projects; (2) a predicted deep ocean by strengthening collaborations within the modeling community, determining needs for interdisciplinary modeling and observing system assessment in the deep ocean; (3) an accessible deep ocean by enhancing open access to innovative low-cost sensors and open-source plans, making deep-ocean data Findable, Accessible, Interoperable, and Reusable, and focusing on capacity development in developing countries; and finally (4) an inspiring and engaging deep ocean by translating science to stakeholders/end users and informing policy and management decisions, including in international waters.
Ciliates along oxyclines of permanently stratified marine water columns

( 2014-02) Edgcomb, Virginia P. ; Pachiadaki, Maria G.

Studies of microbial communities in areas of the world where permanent marine water column oxyclines exist suggest they are ‘hotspots’ of microbial activity, and that these water features and the anoxic waters below them are inhabited by diverse protist taxa, including ciliates. These communities have minimal taxonomic overlap with those in overlying oxic water columns. Some ciliate taxa have been detected in multiple locations where these stable water column oxyclines exist, however, differences in such factors as hydrochemistry in the habitats that have been studied suggest local selection for distinct communities. We compare published data on ciliate communities from studies of deep marine water column oxyclines in Caricao Basin, Venezuela, and the Black Sea, with data from coastal, shallower oxycline waters in Framvaren and Mariager fjords, and from several deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea. Putative symbioses between Bacteria, Archaea, and ciliates observed along these oxyclines suggests a strategy of cooperative metabolism for survival that includes chemosynthetic autotrophy and exchanges of metabolic intermediates or end products between hosts and their prokaryotic partners.
Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins

(BioMed Central, 2015-12-10) Bernhard, Joan M. ; Morrison, Colin R. ; Pape, Ellen ; Beaudoin, David J. ; Todaro, M. Antonio ; Pachiadaki, Maria G. ; Kormas, Konstantinos Ar. ; Edgcomb, Virginia P.

The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth ~3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines. We report observations from sediments of three DHAB (Urania, Discovery, L’Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTrackerTM Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L’Atalante normoxic control sediments were fit, while specimens from L’Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L’Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions. We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time.
Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments

(Frontiers Media, 2014-11-12) Bernhard, Joan M. ; Kormas, Konstantinos Ar. ; Pachiadaki, Maria G. ; Rocke, Emma ; Beaudoin, David J. ; Morrison, Colin R. ; Visscher, Pieter T. ; Cobban, Alec ; Starczak, Victoria R. ; Edgcomb, Virginia P.

Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L’ Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.
Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f

(Frontiers Media, 2020-03-12) Chen, Michael L. ; Becraft, Eric D. ; Pachiadaki, Maria G. ; Brown, Julia M. ; Jarett, Jessica K. ; Gasol, Josep M. ; Ravin, Nikolai V. ; Moser, Duane P. ; Nunoura, Takuro ; Herndl, Gerhard J. ; Woyke, Tanja ; Stepanauskas, Ramunas

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

(Springer Nature, 2020-08-14) Mara, Paraskevi ; Vik, Dean R. ; Pachiadaki, Maria G. ; Suter, Elizabeth A. ; Poulos, Bonnie ; Taylor, Gordon T. ; Sullivan, Matthew B. ; Edgcomb, Virginia P.

Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.
Combined culture-based and culture-independent approaches provide insights into diversity of jakobids, an extremely plesiomorphic eukaryotic lineage

(Frontiers Media, 2015-11-18) Panek, Tomas ; Taborsky, Petr ; Pachiadaki, Maria G. ; Hroudova, Miluse ; Vlcek, Cestmir ; Edgcomb, Virginia P. ; Cepicka, Ivan

We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida), an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids—60 or 80%, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists—Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.
Fungal and prokaryotic activities in the marine subsurface biosphere at Peru Margin and Canterbury Basin inferred from RNA-based analyses and microscopy

(Fromtiers Media, 2016-06-09) Pachiadaki, Maria G. ; Redou, Vanessa ; Beaudoin, David J. ; Burgaud, Gaëtan ; Edgcomb, Virginia P.

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.
Co-designing a multidisciplinary deep-ocean observing programme at the Mid-Atlantic Ridge in the Azores region: a blueprint for synergy in deep ocean research and conservation

(Oxford University Press, 2022-11-02) Pachiadaki, Maria G. ; Janssen, Felix ; Carreiro-Silva, Marina ; Morato, Telmo ; Carreira, Gilberto P ; Frazão, Helena C ; Heimbach, Patrick ; Iglesias, Isabel ; Muller-Karger, Frank E ; Santos, Miguel M ; Smith, Leslie M ; Vardaro, Michael F ; Visser, Fleur ; Waniek, Joanna J ; Zinkann, Ann-Christine ; Colaço, Ana

Under the umbrella of the Deep Ocean Observing Strategy (DOOS) and the All-Atlantic Ocean Observing System (AtlantOS), researchers at the Okeanos—University of the Azores, local stakeholders and authorities, and the deep ocean science community are adopting a co-design approach [which, as highlighted by the Global Ocean Observing System (GOOS), the co-design concept aims to combine the knowledge of diverse experts and stakeholders to create innovative approaches to meet stakeholder needs in ways beyond what could be achieved by any one of those involved working alone] to create a deep-ocean observation project to strengthen deep ocean observing capacities in accordance with users’ and societal needs. The demonstration project discussed below builds on decades of co-design in collaborative efforts in the Azores Archipelago between science, private entities, governmental institutions, and local authorities for science-based management (Santos et al., 1995). Already in the 1980s, several Marine Protected Areas (MPAs) that impose fishing limitations to promote the sustainable use of marine resources were established by this collaborative effort (Santos et al., 1995). During the 2000s, the joint effort between the Regional Government of the Azores and the University of the Azores resulted in the inclusion of 11 sites in the Oslo Paris Convention for the Protection of the North Atlantic (OSPAR; https://www.ospar.org/) MPAs’ network. This made Portugal, and particularly the Azores, a pioneer in the protection of marine biodiversity at an international level (Ribeiro, 2010), and an important progressive player in the ground-breaking OSPAR high-seas MPAs process (Abecasis et al., 2015).
Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

(Nature Research, 2023-02-06) Geller-McGrath, David ; Mara, Paraskevi ; Taylor, Gordon T. ; Suter, Elizabeth ; Edgcomb, Virginia ; Pachiadaki, Maria

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
Impacts of deep-sea mining on microbial ecosystem services

(Association for the Sciences of Limnology and Oceanography, 2020-01-13) Orcutt, Beth N. ; Bradley, James ; Brazelton, William J. ; Estes, Emily R. ; Goordial, Jacqueline M. ; Huber, Julie A. ; Jones, Rose M. ; Mahmoudi, Nagissa ; Marlow, Jeffrey ; Murdock, Sheryl ; Pachiadaki, Maria G.

Interest in extracting mineral resources from the seafloor through deep‐sea mining has accelerated in the past decade, driven by consumer demand for various metals like zinc, cobalt, and rare earth elements. While there are ongoing studies evaluating potential environmental impacts of deep‐sea mining activities, these focus primarily on impacts to animal biodiversity. The microscopic spectrum of seafloor life and the services that this life provides in the deep sea are rarely considered explicitly. In April 2018, scientists met to define the microbial ecosystem services that should be considered when assessing potential impacts of deep‐sea mining, and to provide recommendations for how to evaluate and safeguard these services. Here, we indicate that the potential impacts of mining on microbial ecosystem services in the deep sea vary substantially, from minimal expected impact to loss of services that cannot be remedied by protected area offsets. For example, we (1) describe potential major losses of microbial ecosystem services at active hydrothermal vent habitats impacted by mining, (2) speculate that there could be major ecosystem service degradation at inactive massive sulfide deposits without extensive mitigation efforts, (3) suggest minor impacts to carbon sequestration within manganese nodule fields coupled with potentially important impacts to primary production capacity, and (4) surmise that assessment of impacts to microbial ecosystem services at seamounts with ferromanganese crusts is too poorly understood to be definitive. We conclude by recommending that baseline assessments of microbial diversity, biomass, and, importantly, biogeochemical function need to be considered in environmental impact assessments of deep‐sea mining.
Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins

( 2015-07) Kormas, Konstantinos Ar. ; Pachiadaki, Maria G. ; Karayanni, Hera ; Leadbetter, Edward R. ; Bernhard, Joan M. ; Edgcomb, Virginia P.

The sediment microbiota of the Mediterranean deep-sea anoxic hypersaline basins (DHABs) are understudied relative to communities in the brines and halocline waters. In this study, the active fraction of the prokaryotic community in the halocline sediments of L’ Atalante, Urania, and Discovery DHABs was investigated based on extracted total RNA and 454 pyrosequencing of the 16S rRNA gene. Bacterial and archaeal communities were different in the sediments underlying the halocline waters of the three habitats, reflecting the unique chemical settings of each basin. The relative abundance of unique operational taxonomic units (OTUs) was also different between deep-sea control sediments and sediments underlying DHAB haloclines, suggesting adaptation to the steep DHAB chemical gradients. Only a few OTUs were affiliated to known bacterial halophilic and/or anaerobic groups. Many OTUs, including some of the dominant ones, were related to aerobic taxa. Archaea were detected only in few halocline samples, with lower OTU richness relative to Bacteria, and were dominated by taxa associated with methane cycling. This study suggests that, while metabolically active prokaryotic communities appear to be present in sediments underlying the three DHABs investigated, their diversity and activity are likely to be more reduced in sediments underlying the brines.
Supplemental files from “Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins” (Bernhard et al., submitted, BMC Biology).

( 2015-10-05) Bernhard, Joan M. ; Morrison, Colin R. ; Pape, Ellen ; Beaudoin, David J. ; Todaro, M. Antonio ; Pachiadaki, Maria G. ; Kormas, Konstantinos Ar. ; Edgcomb, Virginia P.

Link provides access to supplemental tables and figures to our manuscript regarding metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins (DHABs). Specimens shown in supplemental figures are loriciferans collected from control and lower halocline sediments of L'Atalante Basin and Discovery Basin. Further details appear in Bernhard et al. (submitted).

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