1
|
Parsons RJ, Liu S, Longnecker K, Yongblah K, Johnson C, Bolaños LM, Comstock J, Opalk K, Kido Soule MC, Garley R, Carlson CA, Temperton B, Bates NR. Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda. Front Microbiol 2023; 14:1287477. [PMID: 38179459 PMCID: PMC10765504 DOI: 10.3389/fmicb.2023.1287477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024] Open
Abstract
Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.
Collapse
Affiliation(s)
- Rachel J. Parsons
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Julie Ann Wrigley Global Futures Laboratory, School of Ocean Futures, Arizona State University, Tempe, AZ, United States
| | - Shuting Liu
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
- Department of Environmental and Sustainability Sciences, Kean University, Union, NJ, United States
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Kevin Yongblah
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Department of Biology, University of Syracuse, Syracuse, NY, United States
| | - Carys Johnson
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
| | - Luis M. Bolaños
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
| | - Melissa C. Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Rebecca Garley
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Julie Ann Wrigley Global Futures Laboratory, School of Ocean Futures, Arizona State University, Tempe, AZ, United States
| | - Craig A. Carlson
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Nicholas R. Bates
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Julie Ann Wrigley Global Futures Laboratory, School of Ocean Futures, Arizona State University, Tempe, AZ, United States
| |
Collapse
|
2
|
Goffredi SK, Panossian B, Brzechffa C, Field N, King C, Moggioli G, Rouse GW, Martín-Durán JM, Henry LM. A dynamic epibiont community associated with the bone-eating polychaete genus Osedax. mBio 2023; 14:e0314022. [PMID: 37382438 PMCID: PMC10470745 DOI: 10.1128/mbio.03140-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/08/2023] [Indexed: 06/30/2023] Open
Abstract
Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.
Collapse
Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Camille Brzechffa
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Naomi Field
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Chad King
- Monterey Bay National Marine Sanctuary, Monterey, California, USA
| | - Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg W. Rouse
- Scripps Oceanography, University of California, La Jolla, California, USA
| | - José M. Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Lee M. Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
3
|
Lin YT, Xu T, Ip JCH, Sun Y, Fang L, Luan T, Zhang Y, Qian PY, Qiu JW, Qian PY, Qiu JW. Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis. Zool Res 2023; 44:106-125. [PMID: 36419378 PMCID: PMC9841196 DOI: 10.24272/j.issn.2095-8137.2022.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.
Collapse
Affiliation(s)
- Yi-Tao Lin
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yanan Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ling Fang
- Instrumental Analysis & Research Center, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China,Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China,E-mail:
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China,
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Borges FO, Sampaio E, Santos CP, Rosa R. Impacts of Low Oxygen on Marine Life: Neglected, but a Crucial Priority for Research. THE BIOLOGICAL BULLETIN 2022; 243:104-119. [PMID: 36548969 DOI: 10.1086/721468] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
AbstractGlobal ocean O2 content has varied significantly across the eons, both shaping and being shaped by the evolutionary history of life on planet Earth. Indeed, past O2 fluctuations have been associated with major extinctions and the reorganization of marine biota. Moreover, its most recent iteration-now anthropogenically driven-represents one of the most prominent challenges for both marine ecosystems and human societies, with ocean deoxygenation being regarded as one of the main drivers of global biodiversity loss. Yet ocean deoxygenation has received far less attention than concurrent environmental variables of marine climate change, namely, ocean warming and acidification, particularly in the field of experimental marine ecology. Together with the lack of consistent criteria defining gradual and acute changes in O2 content, a general lack of multifactorial studies featuring all three drivers and their interactions prevents an adequate interpretation of the potential effects of extreme and gradual deoxygenation. We present a comprehensive overview of the interplay between O2 and marine life across space and time and discuss the current knowledge gaps and future steps for deoxygenation research. This work may also contribute to the ongoing call for an integrative perspective on the combined effects of these three drivers of change for marine organisms and ecosystems worldwide.
Collapse
|
5
|
Symbiont Community Composition in Rimicaris kairei Shrimps from Indian Ocean Vents with Notes on Mineralogy. Appl Environ Microbiol 2022; 88:e0018522. [PMID: 35404070 PMCID: PMC9040608 DOI: 10.1128/aem.00185-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata, which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei. Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria. We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata, such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses. IMPORTANCE Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals of Atlantic and Indian Oceans, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. Here, we characterize the Rimicaris kairei symbiosis by combining molecular, microscopic, and elemental analyses, making comparisons with those of the Atlantic species possible for the first time. Although most symbiotic partners remained consistent across the two oceans, some differences were recognized in symbiont lineages, as well as in the mechanisms behind the formation of two color morphs with distinct mineralogies. Our results shed new light on relationships among mineralogy, environmental factors, and microbial communities that are useful for understanding other deep-sea symbioses in the future.
Collapse
|
6
|
Jiang Q, Jing H, Jiang Q, Zhang Y. Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps. MARINE POLLUTION BULLETIN 2022; 176:113458. [PMID: 35217425 DOI: 10.1016/j.marpolbul.2022.113458] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 02/10/2022] [Indexed: 05/10/2023]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.
Collapse
Affiliation(s)
- QiuYun Jiang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China.
| | - QiuLong Jiang
- The College of Information, Mechanical and Electrical Engineering, Shanghai Normal University, Shanghai 201400, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
7
|
Suter EA, Pachiadaki M, Taylor GT, Edgcomb VP. Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters. Front Microbiol 2022; 12:764605. [PMID: 35069470 PMCID: PMC8770914 DOI: 10.3389/fmicb.2021.764605] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 01/04/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Elizabeth A Suter
- Biology, Chemistry & Environmental Studies Department, Center for Environmental Research and Coastal Oceans Monitoring, Molloy College, Rockville Centre, NY, United States.,School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Maria Pachiadaki
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Virginia P Edgcomb
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| |
Collapse
|
8
|
Yadav S, Koenen M, Bale N, Sinninghe Damsté JS, Villanueva L. The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:899-910. [PMID: 34668338 DOI: 10.1111/1758-2229.13012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.
Collapse
Affiliation(s)
- Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Nicole Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| |
Collapse
|
9
|
Pavlovska M, Prekrasna I, Dykyi E, Zotov A, Dzhulai A, Frolova A, Slobodnik J, Stoica E. Niche partitioning of bacterial communities along the stratified water column in the Black Sea. Microbiologyopen 2021; 10:e1195. [PMID: 34180601 PMCID: PMC8217838 DOI: 10.1002/mbo3.1195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.
Collapse
Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine.,National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine
| | - Andrii Zotov
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,State Institution Institute of Marine Biology of the NAS of Ukraine, Odesa, Ukraine
| | - Artem Dzhulai
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania
| |
Collapse
|
10
|
van Vliet DM, von Meijenfeldt FB, Dutilh BE, Villanueva L, Sinninghe Damsté JS, Stams AJ, Sánchez‐Andrea I. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environ Microbiol 2021; 23:2834-2857. [PMID: 33000514 PMCID: PMC8359478 DOI: 10.1111/1462-2920.15265] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.
Collapse
Affiliation(s)
- Daan M. van Vliet
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for LifeUtrecht University, Padualaan 8, 3584 CHUtrechtNetherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht University, Princetonlaan 8A, 3584 CBUtrechtNetherlands
| | - Alfons J.M. Stams
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de Gualtar, 4710‐057BragaPortugal
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| |
Collapse
|
11
|
Cambon-Bonavita MA, Aubé J, Cueff-Gauchard V, Reveillaud J. Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria. MICROBIOME 2021; 9:87. [PMID: 33845886 PMCID: PMC8042907 DOI: 10.1186/s40168-021-01045-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations. RESULTS Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. CONCLUSION These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.
Collapse
Affiliation(s)
- Marie-Anne Cambon-Bonavita
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Johanne Aubé
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Julie Reveillaud
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
- MIVEGEC, Univ. Montpellier, INRAe, CNRS, IRD, Montpellier, France
| |
Collapse
|
12
|
Chen M, Jiao YY, Zhang YQ, Krumholz LR, Ren JX, Li ZH, Zhao LY, Song HT, Lu JD. Succession of sulfur bacteria during decomposition of cyanobacterial bloom biomass in the shallow Lake Nanhu: An ex situ mesocosm study. CHEMOSPHERE 2020; 256:127101. [PMID: 32450355 DOI: 10.1016/j.chemosphere.2020.127101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/26/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Previous studies of the dynamics of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have focused on deep stratified lakes. The objective of this study is to present an in-depth investigation of the structure and dynamics of sulfur bacteria (including SRB and SOB) in the water column of shallow freshwater lakes. A cyanobacterial bloom biomass (CBB)-amended mesocosm experiment was conducted in this study, in which water was taken from a shallow eutrophic lake with sulfate levels near 40 mg L-1. Illumina sequencing was used to investigate SRB and SOB species involved in CBB decomposition and the effects of the increases in sulfate input on the water column microbial community structure. The accumulation of dissolved sulfide (∑H2S) produced by SRB during CBB decomposition stimulated the growth of SOB, and ∑H2S was then oxidized back to sulfate by SOB in the water column. Chlorobaculum sequences (the main SOB species in the study) were significantly influenced by increases in sulfate input, with relative abundance increasing approximately four-fold in treatments amended with 40 mg L-1 sulfate (referred to as 40S) when compared to the treatment without additional sulfate addition (referred to as CU). Additionally, an increase in SOB number was observed from day 26-37, concurrent with the decrease in SRB number, indicating the succession of sulfur bacteria. These findings suggest that biological sulfur oxidation and succession of sulfur bacteria occur in the water column during CBB decomposition in shallow freshwater ecosystems, and the increases in sulfate input stimulate microbial sulfur oxidation.
Collapse
Affiliation(s)
- Mo Chen
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yi-Ying Jiao
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of Technology, Wuhan, China
| | - Ya-Qing Zhang
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Lee R Krumholz
- Department of Botany & Microbiology, University of Oklahoma, Norman, OK, USA
| | - Jun-Xian Ren
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Zhao-Hua Li
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Li-Ya Zhao
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Hui-Ting Song
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Jin-Deng Lu
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, 430062, China.
| |
Collapse
|
13
|
Yadav S, Villanueva L, Bale N, Koenen M, Hopmans EC, Damsté JSS. Physiological, chemotaxonomic and genomic characterization of two novel piezotolerant bacteria of the family Marinifilaceae isolated from sulfidic waters of the Black Sea. Syst Appl Microbiol 2020; 43:126122. [PMID: 32847788 DOI: 10.1016/j.syapm.2020.126122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 11/17/2022]
Abstract
Diversity analyses of microbial enrichments obtained from deep sulfidic water (2000 m) collected from the Black Sea indicated the presence of eleven novel putative lineages of bacteria affiliated to the family Marinifilaceae of the phylum Bacteroidetes. Pure cultures were obtained for four strains (i.e. M1PT, M3P, A4T and 44) of this family, which could be grouped into two different clades based on their 16S rRNA gene sequences. All four strains were Gram-negative, rod-shaped and facultative anaerobic bacteria. The genomes of all strains were sequenced and physiological analyses were performed. All strains utilized a wide range of carbon sources, which was supported by the presence of the pathways involved in carbon utilization encoded by their genomes. The strains were able to grow at elevated hydrostatic pressure (up to 50 MPa), which coincided with increased production of unsaturated and branched fatty acids, and a decrease in hydroxy fatty acids. Intact polar lipid analysis of all four strains showed the production of ornithine lipids, phosphatidylethanolamines and capnine lipids as major intact polar lipids (IPLs). Genes involved in hopanoid biosynthesis were also identified. However, bacteriohopanepolyols (BHPs) were not detected in the strains. Based on distinct physiological, chemotaxonomic, genotypic and phylogenetic differences compared to other members of the genera Ancylomarina and Labilibaculum, it was concluded that strains M1PT and A4T represented two novel species for which the names Ancylomarina euxinus sp. nov. and Labilibaculum euxinus sp. nov., respectively, are proposed.
Collapse
Affiliation(s)
- Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands.
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Nicole Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands
| | - Ellen C Hopmans
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| |
Collapse
|
14
|
Louca S, Scranton MI, Taylor GT, Astor YM, Crowe SA, Doebeli M. Circumventing kinetics in biogeochemical modeling. Proc Natl Acad Sci U S A 2019; 116:11329-11338. [PMID: 31097587 PMCID: PMC6561284 DOI: 10.1073/pnas.1819883116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbial metabolism drives biogeochemical fluxes in virtually every ecosystem. Modeling these fluxes is challenged by the incredible diversity of microorganisms, whose kinetic parameters are largely unknown. In poorly mixed systems, such as stagnant water columns or sediments, however, long-term bulk microbial metabolism may become limited by physical transport rates of substrates across space. Here we mathematically show that under these conditions, biogeochemical fluxes are largely predictable based on the system's transport properties, chemical boundary conditions, and the stoichiometry of metabolic pathways, regardless of the precise kinetics of the resident microorganisms. We formalize these considerations into a predictive modeling framework and demonstrate its use for the Cariaco Basin subeuphotic zone, one of the largest anoxic marine basins worldwide. Using chemical concentration data solely from the upper boundary (depth 180 m) and lower boundary (depth 900 m), but without a priori knowledge of metabolite fluxes, chemical depth profiles, kinetic parameters, or microbial species composition, we predict the concentrations and vertical fluxes of biologically important substances, including oxygen, nitrate, hydrogen sulfide, and ammonium, across the entire considered depth range (180-900 m). Our predictions largely agree with concentration measurements over a period of 14 years ([Formula: see text] = 0.78-0.92) and become particularly accurate during a period where the system was near biogeochemical steady state (years 2007-2009, [Formula: see text] = 0.86-0.95). Our work enables geobiological predictions for a large class of ecosystems without knowledge of kinetic parameters or geochemical depth profiles. Conceptually, our work provides a possible explanation for the decoupling between microbial species composition and bulk metabolic function, observed in various ecosystems.
Collapse
Affiliation(s)
- Stilianos Louca
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403;
- Department of Biology, University of Oregon, Eugene, OR 97403
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Yrene M Astor
- Estación de Investigaciones Marinas de Margarita, Fundación La Salle de Ciencias Naturales, Punta de Piedras, Estado Nueva Esparta, Venezuela
- Institute for Marine Remote Sensing, University of South Florida, Tampa, FL 33701
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
15
|
Abstract
Mn is one of the most abundant redox-sensitive metals on earth. Some microorganisms are known to use Mn(IV) oxide (MnO2) as electron acceptor for the oxidation of organic compounds or hydrogen (H2), but so far the use of sulfide (H2S) has been suggested but not proven. Here we report on a bacterial isolate which grows autotrophically and couples the reduction of MnO2 to the oxidation of H2S or thiosulfate (S2O32−) for energy generation. The isolate, originating from the Black Sea, is a species within the genus Sulfurimonas, which typically occurs with high cell numbers in the vicinity of sulfidic environments [Y. Han, M. Perner, Front. Microbiol. 6, 989 (2015)]. H2S and S2O32− are oxidized completely to sulfate (SO42−) without the accumulation of intermediates. In the culture, Mn(IV) reduction proceeds via Mn(III) and finally precipitation of Ca-rich Mn(II) carbonate [Mn(Ca)CO3]. In contrast to Mn-reducing bacteria, which use organic electron donors or H2, Fe oxides are not observed to support growth, which may either indicate an incomplete gene set or a different pathway for extracellular electron transfer.
Collapse
|
16
|
Chemosynthetic ectosymbionts associated with a shallow-water marine nematode. Sci Rep 2019; 9:7019. [PMID: 31065037 PMCID: PMC6505526 DOI: 10.1038/s41598-019-43517-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/02/2019] [Indexed: 12/26/2022] Open
Abstract
Prokaryotes and free-living nematodes are both very abundant and co-occur in marine environments, but little is known about their possible association. Our objective was to characterize the microbiome of a neglected but ecologically important group of free-living benthic nematodes of the Oncholaimidae family. We used a multi-approach study based on microscopic observations (Scanning Electron Microscopy and Fluorescence In Situ Hybridization) coupled with an assessment of molecular diversity using metabarcoding based on the 16S rRNA gene. All investigated free-living marine nematode specimens harboured distinct microbial communities (from the surrounding water and sediment and through the seasons) with ectosymbiosis seemed more abundant during summer. Microscopic observations distinguished two main morphotypes of bacteria (rod-shaped and filamentous) on the cuticle of these nematodes, which seemed to be affiliated to Campylobacterota and Gammaproteobacteria, respectively. Both ectosymbionts belonged to clades of bacteria usually associated with invertebrates from deep-sea hydrothermal vents. The presence of the AprA gene involved in sulfur metabolism suggested a potential for chemosynthesis in the nematode microbial community. The discovery of potential symbiotic associations of a shallow-water organism with taxa usually associated with deep-sea hydrothermal vents, is new for Nematoda, opening new avenues for the study of ecology and bacterial relationships with meiofauna.
Collapse
|
17
|
Abstract
Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution of the microbial communities in water samples of Lake Faro was performed by both ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and CARD-FISH (Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization) approaches. A correlation between microbial parameters and both environmental variables (i.e., temperature, pH, dissolved oxygen, redox potential, salinity, chlorophyll-a) and mixing conditions was highlighted, with an evident seasonal variability. The most significative differences were detected by ARISA between the mixolimnion and the monimolimnion, and between Spring and Autumn, by considering layer and season as a factor, respectively.
Collapse
|
18
|
Muller-Karger FE, Astor YM, Benitez-Nelson CR, Buck KN, Fanning KA, Lorenzoni L, Montes E, Rueda-Roa DT, Scranton MI, Tappa E, Taylor GT, Thunell RC, Troccoli L, Varela R. The Scientific Legacy of the CARIACO Ocean Time-Series Program. ANNUAL REVIEW OF MARINE SCIENCE 2019; 11:413-437. [PMID: 29889611 DOI: 10.1146/annurev-marine-010318-095150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The CARIACO (Carbon Retention in a Colored Ocean) Ocean Time-Series Program station, located at 10.50°N, 64.66°W, observed biogeochemical and ecological processes in the Cariaco Basin of the southwestern Caribbean Sea from November 1995 to January 2017. The program completed 232 monthly core cruises, 40 sediment trap deployment cruises, and 40 microbiogeochemical process cruises. Upwelling along the southern Caribbean Sea occurs from approximately November to August. High biological productivity (320-628 g C m-2 y-1) leads to large vertical fluxes of particulate organic matter, but only approximately 9-10 g C m-2 y-1 fall to the bottom sediments (∼1-3% of primary production). A diverse community of heterotrophic and chemoautotrophic microorganisms, viruses, and protozoa thrives within the oxic-anoxic interface. A decrease in upwelling intensity from approximately 2003 to 2013 and the simultaneous overfishing of sardines in the region led to diminished phytoplankton bloom intensities, increased phytoplankton diversity, and increased zooplankton densities. The deepest waters of the Cariaco Basin exhibited long-term positive trends in temperature, salinity, hydrogen sulfide, ammonia, phosphate, methane, and silica. Earthquakes and coastal flooding also resulted in the delivery of sediment to the seafloor. The program's legacy includes climate-quality data from suboxic and anoxic habitats and lasting relationships between international researchers.
Collapse
Affiliation(s)
- Frank E Muller-Karger
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Yrene M Astor
- Estación de Investigaciones Marinas de Margarita, Fundación La Salle de Ciencias Naturales, Punta de Piedras, Estado Nueva Esparta, Venezuela
| | - Claudia R Benitez-Nelson
- Department of Earth and Ocean Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Kristen N Buck
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Kent A Fanning
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Laura Lorenzoni
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
- Ocean Biology and Biogeochemistry Program, National Aeronautics and Space Administration, Washington, DC 20546, USA
| | - Enrique Montes
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Digna T Rueda-Roa
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Eric Tappa
- Department of Earth and Ocean Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Robert C Thunell
- Department of Earth and Ocean Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Luis Troccoli
- Instituto de Investigaciones Cientificas, Universidad de Oriente, Boca Del Rio, Estado Nueva Esparta, Venezuela
| | - Ramon Varela
- Estación de Investigaciones Marinas de Margarita, Fundación La Salle de Ciencias Naturales, Punta de Piedras, Estado Nueva Esparta, Venezuela
| |
Collapse
|
19
|
Sollai M, Villanueva L, Hopmans EC, Reichart G, Sinninghe Damsté JS. A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. GEOBIOLOGY 2019; 17:91-109. [PMID: 30281902 PMCID: PMC6586073 DOI: 10.1111/gbi.12316] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.
Collapse
Affiliation(s)
- Martina Sollai
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Laura Villanueva
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Ellen C. Hopmans
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Gert‐Jan Reichart
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| |
Collapse
|
20
|
Apremont V, Cambon-Bonavita MA, Cueff-Gauchard V, François D, Pradillon F, Corbari L, Zbinden M. Gill chamber and gut microbial communities of the hydrothermal shrimp Rimicaris chacei Williams and Rona 1986: A possible symbiosis. PLoS One 2018; 13:e0206084. [PMID: 30388125 PMCID: PMC6214521 DOI: 10.1371/journal.pone.0206084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/06/2018] [Indexed: 11/18/2022] Open
Abstract
Rimicaris chacei Williams and Rona 1986, formerly named as Chorocaris chacei, is a caridean shrimp living in deep-sea hydrothermal ecosystems. This shrimp is endemic to the Mid Atlantic Ridge (MAR) and lives at the periphery of aggregates of its well-known congeneric R. exoculata Williams and Rona 1986. Contrasting with the very dense and mobile clusters formed by R. exoculata, R. chacei lives in small groups of several individuals that are not very mobile. Although devoid of the characteristic hypertrophied cephalothorax of R. exoculata, which harbors the ectosymbionts, a microbial community has also been reported in the cephalothorax of R. chacei. Previous data on morphology, behavior and isotopic values indicate a diet based on a combination of feeding on its epibiotic bacteria and scavenging or occasional predation. In this study, our objective was to describe, for the first time, the distribution, morphology and phylogeny of the microbial communities associated with R. chacei. This species is significantly less studied than R. exoculata, but nevertheless represents the only other known example of symbiosis in crustaceans of MAR hydrothermal vent sites. Microbial communities have been observed at the same locations as in R. exoculata (mouthparts, branchiostegites and digestive tract). However, in R. chacei, the surfaces occupied by the bacteria are smaller. The main lineages are affiliated to Epsilon and Gammaproteobacteria in the cephalothorax and to Deferribacteres, Mollicutes, Epsilon and Gammaproteobacteria in the digestive tract. Comparison with the well-described bacterial communities of R. exoculata and hypotheses about the role of these communities in R. chacei are discussed.
Collapse
Affiliation(s)
- Vincent Apremont
- IFREMER, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Unité Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université, MNHN, CNRS, IRD; Equipe Adaptation aux Milieux Extrêmes (AMEX), 7 Quai St Bernard, Paris, France
| | | | - Valérie Cueff-Gauchard
- IFREMER, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - David François
- IFREMER, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Florence Pradillon
- Ifremer centre Bretagne, ZI de la Pointe du Diable, Laboratoire Environnement Profond, REM/EEP/LEP, Plouzané, France
| | - Laure Corbari
- Muséum National d’Histoire naturelle, Institut de Systématique, Évolution, Biodiversité ISYEB—UMR 7205 –CNRS, MNHN, UPMC, EPHE, Paris, France
| | - Magali Zbinden
- Unité Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université, MNHN, CNRS, IRD; Equipe Adaptation aux Milieux Extrêmes (AMEX), 7 Quai St Bernard, Paris, France
- * E-mail:
| |
Collapse
|
21
|
Bellec L, Cambon-Bonavita MA, Cueff-Gauchard V, Durand L, Gayet N, Zeppilli D. A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship. Front Microbiol 2018; 9:2246. [PMID: 30294317 PMCID: PMC6159746 DOI: 10.3389/fmicb.2018.02246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/03/2018] [Indexed: 12/26/2022] Open
Abstract
Deep-sea hydrothermal vent meiofauna have been the focus of recent research and the discovery of an abundant well-adapted free-living marine nematode on the Mid-Atlantic Ridge offers new perspectives on adaptations to the vent environment. Indeed, knowledge concerning biological interactions of microbes and meiofauna in marine extreme environments is scarce, especially for nematodes. In this study, we used microscopic observations [fluorescence in situ hybridization (FISH) and scanning electron microscopy (SEM)] and metabarcoding of 16S rRNA to characterize the bacterial community of the nematode species Oncholaimus dyvae, an overlooked but ecologically important vent organism. Detection of bacteria in the buccal cavity and on the cuticle (SEM) and epibionts in its intestine (FISH) suggests that O. dyvae harbors its own bacterial community. Molecular results and phylogenetic analysis show that bacteria associated with this species are related to symbiotic lineages typical of hydrothermal vent fauna, such as sulfur-oxidizing bacteria related to Epsilonproteobacteria and Gammaproteobacteria. This multi-approach study suggests a potential symbiotic role of bacteria with its nematode host and opens new research perspectives on vent meiofauna.
Collapse
Affiliation(s)
- Laure Bellec
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France.,IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Valérie Cueff-Gauchard
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Lucile Durand
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Nicolas Gayet
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France
| | - Daniela Zeppilli
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France
| |
Collapse
|
22
|
Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea. Appl Environ Microbiol 2018. [PMID: 29523543 DOI: 10.1128/aem.02736-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.
Collapse
|
23
|
Suter EA, Pachiadaki M, Taylor GT, Astor Y, Edgcomb VP. Free‐living chemoautotrophic and particle‐attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Environ Microbiol 2017; 20:693-712. [DOI: 10.1111/1462-2920.13997] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Elizabeth A. Suter
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
- Department of Biological SciencesWagner CollegeStaten Island NY 10301 USA
| | - Maria Pachiadaki
- Woods Hole Oceanographic InstitutionWoods Hole MA USA
- Bigelow Laboratory for Ocean SciencesEast Boothbay ME USA
| | - Gordon T. Taylor
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
| | - Yrene Astor
- Fundación La Salle de Ciencias Naturales, EDIMARPorlamar Nueva Esparta Venezuela
| | | |
Collapse
|
24
|
Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PLoS One 2016; 11:e0168719. [PMID: 28030630 PMCID: PMC5193443 DOI: 10.1371/journal.pone.0168719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/04/2016] [Indexed: 12/13/2022] Open
Abstract
The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.
Collapse
Affiliation(s)
- Tanja Bosak
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Ana de Santiago-Torio
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nicki Watson
- W.M. Keck Microscopy Facility, The Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Mirna Daye
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Roger E Summons
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| |
Collapse
|
25
|
Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, Weckwerth W, Schleper C. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proc Natl Acad Sci U S A 2016; 113:E7937-E7946. [PMID: 27864514 PMCID: PMC5150414 DOI: 10.1073/pnas.1601212113] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile "Ca. Nitrosotalea devanaterra" revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and "Ca Nitrosopelagicus brevis" proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
Collapse
Affiliation(s)
- Melina Kerou
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Pierre Offre
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Luis Valledor
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Sophie S Abby
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Michael Melcher
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Wolfram Weckwerth
- Vienna Metabolomics Center, University of Vienna, A-1090 Vienna, Austria
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria;
| |
Collapse
|
26
|
Kalenitchenko D, Dupraz M, Le Bris N, Petetin C, Rose C, West NJ, Galand PE. Ecological succession leads to chemosynthesis in mats colonizing wood in sea water. THE ISME JOURNAL 2016; 10:2246-58. [PMID: 26905628 PMCID: PMC4989304 DOI: 10.1038/ismej.2016.12] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 12/31/2022]
Abstract
Chemosynthetic mats involved in cycling sulfur compounds are often found in hydrothermal vents, cold seeps and whale falls. However, there are only few records of wood fall mats, even though the presence of hydrogen sulfide at the wood surface should create a perfect niche for sulfide-oxidizing bacteria. Here we report the growth of microbial mats on wood incubated under conditions that simulate the Mediterranean deep-sea temperature and darkness. We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features. We show that the wood surface was first colonized by sulfide-oxidizing bacteria belonging to the Arcobacter genus after only 30 days of immersion. Subsequently, the number of sulfate reducers increased and the dominant Arcobacter phylotype changed. The ecological succession was reflected by a change in the metabolic potential of the community from chemolithoheterotrophs to potential chemolithoautotrophs. Our work provides clear evidence for the chemosynthetic nature of wood fall ecosystems and demonstrates the utility to develop experimental incubation in the laboratory to study deep-sea chemosynthetic mats.
Collapse
Affiliation(s)
- Dimitri Kalenitchenko
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogeochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
| | - Marlène Dupraz
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogeochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
| | - Nadine Le Bris
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogeochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
| | - Carole Petetin
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls sur Mer, France
| | - Christophe Rose
- UMR EEF INRA/UL, Plateforme Technique d'Ecologie et d'Ecophysiologie Forestières (PTEF), INRA-LORRAINE, Champenoux, France
| | - Nyree J West
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls sur Mer, France
| | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogeochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
| |
Collapse
|
27
|
Chan CS, Emerson D, Luther GW. The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations. GEOBIOLOGY 2016; 14:509-528. [PMID: 27392195 DOI: 10.1111/gbi.12192] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.
Collapse
Affiliation(s)
- C S Chan
- Department of Geological Sciences, University of Delaware, and the Delaware Biotechnology Institute, Newark, DE, USA
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - G W Luther
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
| |
Collapse
|
28
|
Meyerhof MS, Wilson JM, Dawson MN, Michael Beman J. Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau. Environ Microbiol 2016; 18:4907-4919. [PMID: 27312889 DOI: 10.1111/1462-2920.13416] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/13/2016] [Indexed: 11/29/2022]
Abstract
Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly.
Collapse
Affiliation(s)
- Matthew S Meyerhof
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Jesse M Wilson
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Michael N Dawson
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - J Michael Beman
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| |
Collapse
|
29
|
Chen M, Li XH, He YH, Song N, Cai HY, Wang C, Li YT, Chu HY, Krumholz LR, Jiang HL. Increasing sulfate concentrations result in higher sulfide production and phosphorous mobilization in a shallow eutrophic freshwater lake. WATER RESEARCH 2016; 96:94-104. [PMID: 27023925 DOI: 10.1016/j.watres.2016.03.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 02/20/2016] [Accepted: 03/13/2016] [Indexed: 06/05/2023]
Abstract
Increasing sulfate input has been seen as an issue in management of aquatic ecosystems, but its influences on eutrophic freshwater lakes is not clear. In this study, it was observed that increasing sulfate concentration without additional cyanobacterial bloom biomass (CBB) addition did not have an obvious effect on element cycling during 1-year continuous flow mesocosm experiments in which water and sediments were taken from a shallow eutrophic lake with sulfate levels near 1 mM. However, following addition of CBB to mesocosms, sulfate-reducing bacteria (SRB) were observed in the water column, and increasing numbers of SRB in the water column were associated with higher sulfate input. Sulfate amendment (0-70 mg L(-1)) also resulted in a larger amount of total dissolved sulfide (peak values of 5.90 ± 0.36 to 7.60 ± 0.12 mg L(-1)) in the water column and acid volatile sulfide (1081.71 ± 69.91 to 1557.98 ± 41.72 mg kg(-1)) in 0-1 cm surface sediments due to sulfate reduction. During the period of CBB decomposition, increasing sulfate levels in the water column were positively correlated with increasing diffusive phosphate fluxes of 1.23 ± 0.32 to 2.17 ± 0.01 mg m(-2) d(-1) at the water-sediment interface. As increases in sulfide and phosphate release rates deteriorated the water quality/ecosystem and even spurred the occurrence of a black water problem in lakes, the control of sulfate input level should be considered for shallow eutrophic lake management, especially during cyanobacterial bloom periods.
Collapse
Affiliation(s)
- Mo Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Graduate University of Chinese Academy of Sciences, China
| | - Xiao-Hong Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Graduate University of Chinese Academy of Sciences, China
| | - Yu-Hong He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Graduate University of Chinese Academy of Sciences, China
| | - Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hai-Yuan Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yun-Tao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Graduate University of Chinese Academy of Sciences, China
| | - Hai-Yan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lee R Krumholz
- Department of Botany & Microbiology, University of Oklahoma, Norman, OK, USA
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| |
Collapse
|
30
|
Steen IH, Dahle H, Stokke R, Roalkvam I, Daae FL, Rapp HT, Pedersen RB, Thorseth IH. Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems. Front Microbiol 2016; 6:1510. [PMID: 26779165 PMCID: PMC4703759 DOI: 10.3389/fmicb.2015.01510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/23/2023] Open
Abstract
In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO4) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH4 and H2S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H2 seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.
Collapse
Affiliation(s)
- Ida H Steen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Frida-Lise Daae
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Hans Tore Rapp
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
| |
Collapse
|
31
|
Spietz RL, Williams CM, Rocap G, Horner-Devine MC. A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary. PLoS One 2015; 10:e0135731. [PMID: 26270047 PMCID: PMC4535773 DOI: 10.1371/journal.pone.0135731] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/26/2015] [Indexed: 11/18/2022] Open
Abstract
Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA−a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L-1. This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L-1), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems.
Collapse
Affiliation(s)
- Rachel L. Spietz
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Cheryl M. Williams
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - M. Claire Horner-Devine
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
32
|
Merkel AY, Korneeva VA, Tarnovetskii IY, Bryukhanov AL, Chasovnikov VK, Taranov EA, Toshchakov SV, Pimenov NV. Structure of the archaeal community in the Black Sea photic zone. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715040128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
33
|
Rodriguez-Mora MJ, Scranton MI, Taylor GT, Chistoserdov AY. The dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing. FEMS Microbiol Ecol 2015. [PMID: 26209697 DOI: 10.1093/femsec/fiv088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Massively parallel tag sequencing was applied to describe the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin. In total, 14 samples from the Cariaco Basin were collected over a period of eight years from two stations. A total of 244 357 unique bacterial V6 amplicons were sequenced. The total number of operational taxonomic units (OTUs) found in this study was 4692, with a range of 511-1491 OTUs per sample. Approximately 95% of the OTUs found in the redox transition zone and anoxic layers of Cariaco are represented by less than 50 amplicons suggesting that only about 5% of the bacterial OTUs are responsible for the bulk of the microbial processes in the basin redox transition and anoxic zones. The same dominant OTUs were observed across all eight years of sampling although periodic fluctuations in their proportion were apparent. No distinctive differences were observed between the bacterial communities from the redox transition and anoxic layers of the Cariaco Basin water column. The largest proportion of amplicons belongs to Gammaproteobacteria represented mostly by sulfide oxidizers, followed by Marine Group A (originally described as SAR406; Gordon and Giovannoni 1996), a group of uncultured bacteria hypothesized to be involved in metal reduction, and sulfate-reducing Deltaproteobacteria. Gammaproteobacteria, Deltaproteobacteria and Marine Group A make up 67-90% of all V6 amplicons sequenced in this study. This strongly suggests that the basin's microbial communities are actively involved in the sulfur-related metabolism and coupling of the sulfur and carbon cycles. According to detrended canonical correspondence analysis, ecological factors such as chemoautotrophy, nitrate and oxidized and reduced sulfur compounds influence the structuring and distribution of the Cariaco microbial communities.
Collapse
Affiliation(s)
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Andrei Y Chistoserdov
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| |
Collapse
|
34
|
Noguerola I, Picazo A, Llirós M, Camacho A, Borrego CM. Diversity of freshwaterEpsilonproteobacteriaand dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake. FEMS Microbiol Ecol 2015. [PMID: 26195601 DOI: 10.1093/femsec/fiv086] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Imma Noguerola
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain
| | - Antonio Picazo
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Edificio de Investigación 'Jeroni Muñoz', Campus de Burjassot, Universitat de Valencia, E-46100, Burjassot, Valencia, Spain
| | - Marc Llirós
- Université Catholique de Louvain, Institut des Sciences de la Vie, Place Croix du Sud, 4/5 L07.07.06, B-1348 Louvain-La-Neuve, Belgium
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Edificio de Investigación 'Jeroni Muñoz', Campus de Burjassot, Universitat de Valencia, E-46100, Burjassot, Valencia, Spain
| | - Carles M Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, Spain
| |
Collapse
|
35
|
Mulec J, Krištůfek V, Chroňáková A, Oarga A, Scharfen J, Šestauberová M. Microbiology of healing mud (fango) from Roman thermae aquae iasae archaeological site (Varaždinske Toplice, Croatia). MICROBIAL ECOLOGY 2015; 69:293-306. [PMID: 25241172 DOI: 10.1007/s00248-014-0491-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/01/2014] [Indexed: 06/03/2023]
Abstract
We found well-preserved, rocky artefacts that had been buried in the healing mud (fango) for more than 1,500 years at the Roman archaeological site at Varaždinske Toplice. This Roman pool with fango sediments and artefacts is fed from hot sulphidic springs. The fango exhibited nearly neutral pH, a high level of organic C, an elevated concentration of heavy metals and a high total microbial biomass, greater than 10(8) cells per gram of dry weight. The dominant microbes, assessed by molecular profiling (denaturing gradient gel electrophoresis), were affiliated with Thiobacillus, Sulfuricurvum, Polaromonas, and Bdellovibrio. Polymerase chain reaction screening for microbial functional guilds revealed the presence of sulphur oxidizers and methanogens but no sulphate reducers. The dominance of four Proteobacterial classes (α-, β-, δ- and ε-Proteobacteria) was confirmed by fluorescence in situ hybridisation; Actinobacteria were less abundant. Cultivable bacteria represented up to 23.4 % of the total bacterial counts when cultivation media was enriched with fango. These bacteria represented the genera Acinetobacter, Aeromonas, Arthrobacter, Comamonas, Ewingella, Flavobacterium, Pseudomonas, Rahnella and Staphylococcus. This study showed that the heterogeneous nature of fango at neutral pH created various microniches, which largely supported microbial life based on sulphur-driven, autotrophic denitrification.
Collapse
Affiliation(s)
- Janez Mulec
- Research Centre of the Slovenian Academy of Sciences and Arts, Karst Research Institute, Titov trg 2, 6230, Postojna, Slovenia,
| | | | | | | | | | | |
Collapse
|
36
|
Berg C, Vandieken V, Thamdrup B, Jürgens K. Significance of archaeal nitrification in hypoxic waters of the Baltic Sea. ISME JOURNAL 2014; 9:1319-32. [PMID: 25423026 DOI: 10.1038/ismej.2014.218] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/25/2014] [Accepted: 10/03/2014] [Indexed: 11/09/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread, and their abundance in many terrestrial and aquatic ecosystems suggests a prominent role in nitrification. AOA also occur in high numbers in oxygen-deficient marine environments, such as the pelagic redox gradients of the central Baltic Sea; however, data on archaeal nitrification rates are scarce and little is known about the factors, for example sulfide, that regulate nitrification in this system. In the present work, we assessed the contribution of AOA to ammonia oxidation rates in Baltic deep basins and elucidated the impact of sulfide on this process. Rate measurements with (15)N-labeled ammonium, CO(2) dark fixation measurements and quantification of AOA by catalyzed reporter deposition-fluorescence in situ hybridization revealed that among the three investigated sites the highest potential nitrification rates (122-884 nmol l(-1)per day) were measured within gradients of decreasing oxygen, where thaumarchaeotal abundance was maximal (2.5-6.9 × 10(5) cells per ml) and CO(2) fixation elevated. In the presence of the archaeal-specific inhibitor GC(7), nitrification was reduced by 86-100%, confirming the assumed dominance of AOA in this process. In samples spiked with sulfide at concentrations similar to those of in situ conditions, nitrification activity was inhibited but persisted at reduced rates. This result together with the substantial nitrification potential detected in sulfidic waters suggests the tolerance of AOA to periodic mixing of anoxic and sulfidic waters. It begs the question of whether the globally distributed Thaumarchaeota respond similarly in other stratified water columns or whether the observed robustness against sulfide is a specific feature of the thaumarchaeotal subcluster present in the Baltic Deeps.
Collapse
Affiliation(s)
- Carlo Berg
- 1] Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany [2] Stockholm University, Science for Life Laboratory, Stockholm, Sweden
| | - Verona Vandieken
- 1] Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany [2] Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Bo Thamdrup
- Nordic Center for Earth Evolution (NordCEE) and Department of Biology, University of Southern Denmark (SDU), Odense, Denmark
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
| |
Collapse
|
37
|
Kubo K, Kojima H, Fukui M. Vertical distribution of major sulfate-reducing bacteria in a shallow eutrophic meromictic lake. Syst Appl Microbiol 2014; 37:510-9. [DOI: 10.1016/j.syapm.2014.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/07/2014] [Accepted: 05/07/2014] [Indexed: 11/26/2022]
|
38
|
Parsons RJ, Nelson CE, Carlson CA, Denman CC, Andersson AJ, Kledzik AL, Vergin KL, McNally SP, Treusch AH, Giovannoni SJ. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environ Microbiol 2014; 17:3481-99. [DOI: 10.1111/1462-2920.12445] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/23/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rachel J. Parsons
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
| | - Craig E. Nelson
- Department of Ecology, Evolution and Marine Biology; Marine Science Institute; University of California; Santa Barbara CA USA
- Center for Microbial Oceanography: Research and Education; Department of Oceanography; University of Hawai‘i at Mānoa; Honolulu HI USA
| | - Craig A. Carlson
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- Department of Ecology, Evolution and Marine Biology; Marine Science Institute; University of California; Santa Barbara CA USA
| | - Carmen C. Denman
- Department of Microbiology; Oregon State University; Corvallis OR USA
- London School of Hygiene and Tropical Medicine; London UK
| | - Andreas J. Andersson
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- Scripps Institution of Oceanography; University of California San Diego; San Diego CA USA
| | - Andrew L. Kledzik
- Department of Marine and Environmental Systems; Florida Institute of Technology; Melbourne FL USA
| | - Kevin L. Vergin
- Department of Microbiology; Oregon State University; Corvallis OR USA
| | - Sean P. McNally
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- College of the Environment and Life Sciences; The University of Rhode Island; Kingston RI USA
| | - Alexander H. Treusch
- Department of Microbiology; Oregon State University; Corvallis OR USA
- Department of Biology; Nordic Centre for Earth Evolution; University of Southern Denmark; Odense Denmark
| | | |
Collapse
|
39
|
Mammitzsch K, Jost G, Jürgens K. Impact of dissolved inorganic carbon concentrations and pH on growth of the chemolithoautotrophic epsilonproteobacterium Sulfurimonas gotlandica GD1T. Microbiologyopen 2014; 3:80-8. [PMID: 24376054 PMCID: PMC3937731 DOI: 10.1002/mbo3.153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/08/2013] [Accepted: 10/22/2013] [Indexed: 11/09/2022] Open
Abstract
Epsilonproteobacteria have been found globally distributed in marine anoxic/sulfidic areas mediating relevant transformations within the sulfur and nitrogen cycles. In the Baltic Sea redox zones, chemoautotrophic epsilonproteobacteria mainly belong to the Sulfurimonas gotlandica GD17 cluster for which recently a representative strain, S. gotlandica GD1(T), could be established as a model organism. In this study, the potential effects of changes in dissolved inorganic carbon (DIC) and pH on S. gotlandica GD1(T) were examined. Bacterial cell abundance within a broad range of DIC concentrations and pH values were monitored and substrate utilization was determined. The results showed that the DIC saturation concentration for achieving maximal cell numbers was already reached at 800 μmol L(-1), which is well below in situ DIC levels. The pH optimum was between 6.6 and 8.0. Within a pH range of 6.6-7.1 there was no significant difference in substrate utilization; however, at lower pH values maximum cell abundance decreased sharply and cell-specific substrate consumption increased.
Collapse
Affiliation(s)
- Kerstin Mammitzsch
- Sektion Biologische Meereskunde, Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, D-18119, Rostock, Germany
| | | | | |
Collapse
|
40
|
Metatranscriptomic analyses of plankton communities inhabiting surface and subpycnocline waters of the Chesapeake Bay during oxic-anoxic-oxic transitions. Appl Environ Microbiol 2013; 80:328-38. [PMID: 24162577 DOI: 10.1128/aem.02680-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We used metatranscriptomics to study the gene transcription patterns of microbial plankton (0.2 to 64 μm) at a mesohaline station in the Chesapeake Bay under transitions from oxic to anoxic waters in spring and from anoxic to oxic waters in autumn. Samples were collected from surface (i.e., above pycnocline) waters (3 m) and from waters beneath the pycnocline (16 to 22 m) in both 2010 and 2011. Metatranscriptome profiles based on function and potential phylogeny were different between 2010 and 2011 and strongly variable in 2011. This difference in variability corresponded with a highly variable ratio of eukaryotic to bacterial sequences (0.3 to 5.5), reflecting transient algal blooms in 2011 that were absent in 2010. The similarity between metatranscriptomes changed at a lower rate during the transition from oxic to anoxic waters than after the return to oxic conditions. Transcripts related to photosynthesis and low-affinity cytochrome oxidases were significantly higher in shallow than in deep waters, while in deep water genes involved in anaerobic metabolism, particularly sulfate reduction, succinyl coenzyme A (succinyl-CoA)-to-propionyl-CoA conversion, and menaquinone synthesis, were enriched relative to in shallow waters. Expected transitions in metabolism between oxic and anoxic deep waters were reflected in elevated levels of anaerobic respiratory reductases and utilization of propenediol and acetoin. The percentage of archaeal transcripts increased in both years in late summer (from 0.1 to 4.4% of all transcripts in 2010 and from 0.1 to 6.2% in 2011). Denitrification-related genes were expressed in a predicted pattern during the oxic-anoxic transition. Overall, our data suggest that Chesapeake Bay microbial assemblages express gene suites differently in shallow and deep waters and that differences in deep waters reflect variable redox states.
Collapse
|
41
|
Bozo-Hurtado L, García-Amado MA, Chistoserdov A, Varela R, Narvaez JJ, Colwell R, Suárez P. Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments. AQUATIC BIOSYSTEMS 2013; 9:17. [PMID: 23981583 PMCID: PMC3765856 DOI: 10.1186/2046-9063-9-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/24/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30' N, 64°40' W), B (10°40' N, 64°45' W) and D (10°43'N, 64°32'W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. RESULTS DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. CONCLUSIONS In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.
Collapse
Affiliation(s)
- Lorelei Bozo-Hurtado
- Departamento de Biología de Organismos, Universidad Simón Bolívar, Caracas, Venezuela
| | - M Alexandra García-Amado
- Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Andrei Chistoserdov
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Ramon Varela
- EDIMAR, Fundación La Salle, Margarita, Venezuela
| | | | - Rita Colwell
- University of Maryland, College Park, Maryland, USA
| | - Paula Suárez
- Departamento de Biología de Organismos, Universidad Simón Bolívar, Caracas, Venezuela
| |
Collapse
|
42
|
Goffredi SK, Gregory A, Jones WJ, Morella NM, Sakamoto RI. Ontogenetic variation in epibiont community structure in the deep-sea yeti crab, Kiwa puravida: convergence among crustaceans. Mol Ecol 2013; 23:1457-1472. [PMID: 23952239 DOI: 10.1111/mec.12439] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/29/2013] [Accepted: 07/02/2013] [Indexed: 01/08/2023]
Abstract
Recent investigations have demonstrated that unusually 'hairy' yeti crabs within the family Kiwaidae associate with two predominant filamentous bacterial families, the Epsilon and Gammaproteobacteria. These analyses, however, were based on samples collected from a single body region, the setae of pereopods. To more thoroughly investigate the microbiome associated with Kiwa puravida, a yeti crab species from Costa Rica, we utilized barcoded 16S rRNA amplicon pyrosequencing, as well as microscopy and terminal restriction fragment length polymorphism analysis. Results indicate that, indeed, the bacterial community on the pereopods is far less diverse than on the rest of the body (Shannon indices ranged from 1.30-2.02 and 2.22-2.66, respectively). Similarly, the bacterial communities associated with juveniles and adults were more complex than previously recognized, with as many as 46 bacterial families represented. Ontogenetic differences in the microbial community, from egg to juvenile to adult, included a dramatic under-representation of the Helicobacteraceae and higher abundances of both Thiotrichaceae and Methylococcaceae for the eggs, which paralleled patterns observed in another bacteria-crustacean symbiosis. The degree to which abiotic and biotic feedbacks influence the bacterial community on the crabs is still not known, but predictions suggest that both the local environment and host-derived factors influence the establishment and maintenance of microbes associated with the surfaces of aquatic animals.
Collapse
Affiliation(s)
- Shana K Goffredi
- Biology Department, Occidental College, Los Angeles, CA, 90041, USA
| | | | | | | | | |
Collapse
|
43
|
Teixeira LCRS, Yeargeau E, Balieiro FC, Piccolo MC, Peixoto RS, Greer CW, Rosado AS. Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica. PLoS One 2013; 8:e66109. [PMID: 23840411 PMCID: PMC3688718 DOI: 10.1371/journal.pone.0066109] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 05/06/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
Collapse
Affiliation(s)
- Lia C. R. S. Teixeira
- Laboratório de Ecologia Microbiana Molecular, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Etienne Yeargeau
- Biotechnology Research Institute, National Research Council of Canada, Montréal, QC, Canada
| | - Fabiano C. Balieiro
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) solos, Rio de Janeiro, RJ, Brasil
| | - Marisa C. Piccolo
- Laboratório de Ciclagem de Nutrientes, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, SP, Brasil
| | - Raquel S. Peixoto
- Laboratório de Ecologia Microbiana Molecular, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Charles W. Greer
- Biotechnology Research Institute, National Research Council of Canada, Montréal, QC, Canada
| | - Alexandre S. Rosado
- Laboratório de Ecologia Microbiana Molecular, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
- * E-mail:
| |
Collapse
|
44
|
Rodriguez-Mora MJ, Scranton MI, Taylor GT, Chistoserdov AY. Bacterial community composition in a large marine anoxic basin: a Cariaco Basin time-series survey. FEMS Microbiol Ecol 2013; 84:625-39. [PMID: 23398056 DOI: 10.1111/1574-6941.12094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 01/18/2013] [Accepted: 02/05/2013] [Indexed: 11/30/2022] Open
Abstract
Redox transition zones play a crucial role in biogeochemical cycles of several major elements. Because microorganisms mediate many reactions of these cycles, they actively participate in establishing geochemical gradients. In turn, the geochemical gradients structure microbial communities. We studied the interrelationship between the bacterial community structure and the geochemical gradient in the Cariaco Basin, the largest truly marine anoxic basin. This study's dataset includes bacterial community composition in 113 water column samples as well as the data for environmental variables (gradients of oxygen, hydrogen sulfide, sulfite, thiosulfate, ammonia, nitrate, nitrite, dissolved manganese and iron, dark CO2 fixation, and bacterial abundance) collected between 1997 and 2006. Several prominent bacterial groups are present throughout the entire water column. These include members of Gamma-, Delta-, and Epsilonproteobacteria, as well as members of the Marine Group A, the candidate divisions OP11 and Car731c. Canonical correspondence analysis indicated that microbial communities segregate along vectors representing oxygenated conditions, nitrite, nitrate and anoxic environments represented by chemoautotrophy, ammonia, sulfite, and hydrogen sulfide.
Collapse
|
45
|
SUP05 dominates the Gammaproteobacterial sulfur oxidizer assemblages in pelagic redoxclines of the central Baltic and Black Seas. Appl Environ Microbiol 2013; 79:2767-76. [PMID: 23417000 DOI: 10.1128/aem.03777-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Gammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, the in situ abundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescence in situ hybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (cbbM) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. The cbbM transcripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.
Collapse
|
46
|
King GM, Smith CB, Tolar B, Hollibaugh JT. Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern gulf of Mexico. Front Microbiol 2013; 3:438. [PMID: 23346078 PMCID: PMC3548560 DOI: 10.3389/fmicb.2012.00438] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/19/2012] [Indexed: 01/20/2023] Open
Abstract
16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity, and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM) sampled in March 2010. Statistical analyses showed that samples from depths ≤100 m differed distinctly from deeper samples. SAR 11 α-Proteobacteria and Bacteroidetes dominated communities at depths ≤100 m, which were characterized by high α-Proteobacteria/γ-Proteobacteria ratios (α/γ > 1.7). Thaumarchaeota, Firmicutes, and δ-Proteobacteria were relatively abundant in deeper waters, and α/γ ratios were low (<1). Canonical correlation analysis indicated that δ- and γ-Proteobacteria, Thaumarchaeota, and Firmicutes correlated positively with depth; α-Proteobacteria and Bacteroidetes correlated positively with temperature and dissolved oxygen; Actinobacteria, β-Proteobacteria, and Verrucomicrobia correlated positively with a measure of suspended particles. Diversity indices did not vary with depth or other factors, which indicated that richness and evenness elements of bacterioplankton communities might develop independently of nGoM physical-chemical variables. Phylogenetic community structure as measured by the net relatedness (NRI) and nearest taxon (NTI) indices also did not vary with depth. NRI values indicated that most of the communities were comprised of OTUs more distantly related to each other in whole community comparisons than expected by chance. NTI values derived from phylogenetic distances of the closest neighbor for each OTU in a given community indicated that OTUs tended to occur in clusters to a greater extent than expected by chance. This indicates that "habitat filtering" might play an important role in nGoM bacterioplankton species assembly, and that such filtering occurs throughout the water column.
Collapse
Affiliation(s)
- Gary M King
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
| | | | | | | |
Collapse
|
47
|
Hawley AK, Kheirandish S, Mueller A, Leung HTC, Norbeck AD, Brewer HM, Pasa-Tolic L, Hallam SJ. Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters. Methods Enzymol 2013; 531:305-29. [PMID: 24060128 DOI: 10.1016/b978-0-12-407863-5.00016-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.
Collapse
Affiliation(s)
- Alyse K Hawley
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | | | | | | | | | | |
Collapse
|
48
|
La Cono V, La Spada G, Arcadi E, Placenti F, Smedile F, Ruggeri G, Michaud L, Raffa C, De Domenico E, Sprovieri M, Mazzola S, Genovese L, Giuliano L, Slepak VZ, Yakimov MM. Partaking of Archaea to biogeochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy). Environ Microbiol 2012; 15:1717-33. [PMID: 23253149 DOI: 10.1111/1462-2920.12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 11/22/2012] [Accepted: 11/23/2012] [Indexed: 11/29/2022]
Abstract
We used a combination of molecular and microbiological approaches to determine the activity, abundance and diversity of archaeal populations inhabiting meromictic saline Lake Faro (Messina, Italy). Analysis of archaeal 16S rRNA, amoA, accA and hbd genes and transcripts revealed that sub- and anoxic layers of Lake Faro are primarily inhabited by the organisms related to the clusters of Marine Group I.1a of Thaumarchaeota frequently recovered from oxygen-depleted marine ecosystems. These organisms dominated the metabolically active archaea down to the bottom of the lake, indicating their adaptation to recurrent changes in the levels of water column hypoxia. The upper microaerobic layer of Lake Faro redoxcline has the maximal rates of dark primary production much lower than those of other previously studied pelagic redoxclines, but comparable to the values of meso- and bathypelagic areas of Mediterranean Sea. Application of bacterial inhibitors, especially azide, significantly declined the CO2 fixation rates in the low interface and monimolimnion, whereas archaea-specific inhibitor had effect only in upper part of the redoxcline. Based on these findings, we hypothesize that dark bicarbonate fixation in suboxic zone of Lake Faro results mainly from archaeal activity which is affected by the predicted lack in oxygen in lower layers.
Collapse
Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
Collapse
Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
| |
Collapse
|
50
|
Bruckner CG, Mammitzsch K, Jost G, Wendt J, Labrenz M, Jürgens K. Chemolithoautotrophic denitrification of epsilonproteobacteria in marine pelagic redox gradients. Environ Microbiol 2012; 15:1505-13. [PMID: 23013279 DOI: 10.1111/j.1462-2920.2012.02880.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 07/13/2012] [Accepted: 08/23/2012] [Indexed: 11/29/2022]
Abstract
Pelagic marine oxygen-depleted zones often exhibit a redox gradient, caused by oxygen depletion due to biological demand exceeding ventilation, and the accumulation of reduced chemical species, such as hydrogen sulfide. These redox gradients harbour a distinct assemblage of epsilonproteobacteria capable of fixing carbon dioxide autotrophically in the dark and potentially of utilizing hydrogen sulfide chemolithotrophically by oxidation with nitrate. Together, these two processes are referred to as chemolithoautotrophic denitrification. The focus of this study was the recently isolated and cultivated representative strain of pelagic epsilonproteobacteria, 'Sulfurimonas gotlandica' strain GD1, specifically dark carbon dioxide fixation and its substrate turnovers during chemolithotrophic denitrification. By connecting these processes stoichiometrically and comparing the results with those obtained for dark carbon dioxide fixation and nutrient concentrations measured in pelagic redox gradients of the Baltic Sea, we were able to estimate the role of chemolithoautotrophic denitrification in the environment. Evidence is provided for a defined zone where chemolithoautotrophic denitrification of these epsilonproteobacteria allows the complete removal of nitrate and hydrogen sulfide from the water column. This water layer is roughly equivalent in thickness to the average overlapping region of the two substrates, but slightly larger. Such a difference may be explained by a variety of reasons, including, e.g. utilization of substrates present at concentrations below the detection limit, alternative usage of other substrates as thiosulfate or nitrous oxide, or comparable activities of other microbes. However, the combined results of in vitro and in situ studies strongly suggest that epsilonproteobacteria are primarily responsible for hydrogen sulfide and nitrate removal from pelagic Baltic Sea redox gradients.
Collapse
Affiliation(s)
- Christian G Bruckner
- Department of Biological Oceanography, Leibniz-Institute for Baltic Sea Research Warnemünde, Seestrasse 15, D-18119, Rostock, Germany.
| | | | | | | | | | | |
Collapse
|