Riddles in the cold: Antarctic endemism and microbial succession impact methane cycling in the Southern Ocean

Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70 m × 1 m) microbial mat formed at 10 m water depth in the Ross Sea, Antarctica which we identify here to be a high latitude hydrogen sulfide and methane seep. Through 16S rRNA gene analysis on samples collected 1 year and 5 years after the methane seep formed, we identify the taxa involved in the Antarctic methane cycle and quantify the response rate of the microbial community to a novel input of methane. One year after the seep formed, ANaerobic MEthane oxidizing archaea (ANME), the dominant sink of methane globally, were absent. Five years later, ANME were found to make up to 4% of the microbial community, however the dominant member of this group observed (ANME-1) were unexpected considering the cold temperature (−1.8°C) and high sulfate concentrations (greater than 24 mM) present at this site. Additionally, the microbial community had not yet formed a sufficient filter to mitigate the release of methane from the sediment; methane flux from the sediment was still significant at 3.1 mmol CH 4 m −2 d −1 . We hypothesize that this 5 year time point represents an early successional stage of the microbiota in response to methane input. This study provides the first report of the evolution of a seep system from a non-seep environment, and reveals that the rate of microbial succession may have an unrealized impact on greenhouse gas emission from marine methane reservoirs.

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Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta

Microorganisms ◽

10.3390/microorganisms8081181 ◽

2020 ◽

Vol 8 (8) ◽

pp. 1181

Author(s):

Reynaldo Núñez Salazar ◽

Carlos Aguirre ◽

Jorge Soto ◽

Pamela Salinas ◽

Carlos Salinas ◽

...

Keyword(s):

Microbial Community ◽

High Altitude ◽

Water Column ◽

Physicochemical Parameters ◽

Microbial Community Composition ◽

Atacama Desert ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Lake System ◽

Influence Of Water

Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.

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Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession

10.7287/peerj.preprints.3498 ◽

2017 ◽

Author(s):

Patrick J Kearns ◽

Ashley Shade

Keyword(s):

Microbial Community ◽

Case Studies ◽

Reference Conditions ◽

Growth Strategy ◽

Rrna Gene ◽

Microbial Succession ◽

Gene Copies ◽

Community Weighted Mean ◽

And Function ◽

Press Disturbance

Understanding the relationship between microbial community structure and function is a major challenge in microbial ecology. Recent work has shown that community weighted mean 16S rRNA gene copies, as a proxy for heterotrophic growth strategy, is a microbial community trait that decreases predictably over successional trajectories that are underpinned by changes in resource availability. However, it has been challenging to identify other microbial traits that are predictive of community functions and have consistent patterns with succession. Trait-based patterns of secondary succession (e.g., after a disturbance) are less often considered, and these responses may be underpinned by abiotic drivers other than changes in resources. In this perspectives piece, we present hypotheses about microbial traits important for microbial succession in resource-based and post-press disturbance scenarios, as synthesized from previous works and extended within this work. Using four case studies, we compare two traits, heterotrophic strategy and dormancy potential, and two different types of succession, resource-based (endogenous heterotrophic) and post-press. There were decreases in weighted ribosomal operon counts and in dormancy genes over resource-based succession. Both traits also were lower in post-press succession as compared to reference conditions, but increased with time from disturbance. Thus, dormancy potential may be an additional trait that changes predictably with succession. Finally, considering changes in microbial community traits over post-press succession is as important as over resource-based succession. These patterns need be interpreted carefully and reference and recovering samples can be collected to improve interpretation of changes in community traits over post-press succession.

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Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

mBio ◽

10.1128/mbio.01348-15 ◽

2015 ◽

Vol 6 (6) ◽

Cited By ~ 35

Author(s):

David H. Case ◽

Alexis L. Pasulka ◽

Jeffrey J. Marlow ◽

Benjamin M. Grupe ◽

Lisa A. Levin ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Methane Flux ◽

Rrna Gene ◽

Methane Seep ◽

Methane Seeps ◽

Methane Seepage ◽

Wide Range ◽

Sediment Bottom ◽

Rrna Gene Sequencing ◽

Geologic Record

ABSTRACTMarine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g.,Chloroflexioperational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages.IMPORTANCESince their discovery in 1984, the global distribution and importance of marine methane seeps have become increasingly clear. Much of our understanding of methane seep microorganisms—from metabolisms to community ecology—has stemmed from detailed studies of seep sediments. However, it has become apparent that carbonates represent a volumetrically significant habitat substrate at methane seeps. Through combinedin situcharacterization and incubation experiments, this study demonstrates that carbonates host microbial assemblages distinct from and more diverse than those of other seep habitats. This emphasizes the importance of seep carbonates as biodiversity locales. Furthermore, we demonstrate that carbonate-associated microbial assemblages are well adapted to withstand fluctuations in methane seepage, and we gain novel insight into particular taxa that are responsive (or recalcitrant) to changes in seep conditions.

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Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession

10.7287/peerj.preprints.3498v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Patrick J Kearns ◽

Ashley Shade

Keyword(s):

Microbial Community ◽

Case Studies ◽

Reference Conditions ◽

Growth Strategy ◽

Rrna Gene ◽

Microbial Succession ◽

Gene Copies ◽

Community Weighted Mean ◽

And Function ◽

Press Disturbance

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Endolithic Microbial Habitats Hosted in Carbonate Nodules Currently Forming within Sediment at a High Methane Flux Site in the Sea of Japan

Geosciences ◽

10.3390/geosciences9110463 ◽

2019 ◽

Vol 9 (11) ◽

pp. 463 ◽

Cited By ~ 1

Author(s):

Katsunori Yanagawa ◽

Fumito Shiraishi ◽

Yusuke Tanigawa ◽

Toshinari Maeda ◽

Nurul Asyifah Mustapha ◽

...

Keyword(s):

Microbial Community ◽

Sea Of Japan ◽

Microbial Community Composition ◽

Methane Flux ◽

The Sea Of Japan ◽

Anaerobic Oxidation Of Methane ◽

Methane Seep ◽

Carbon Isotopic ◽

Oxidation Of Methane ◽

Microbial Habitat

Concretionary carbonates in deep-sea methane seep fields are formed as a result of microbial methane degradation, called anaerobic oxidation of methane (AOM). Recently, active microorganisms, including anaerobic methanotrophic archaea, were discovered from methane seep-associated carbonate outcroppings on the seafloor. However sedimentary buried carbonate nodules are a hitherto unknown microbial habitat. In this study, we investigated the microbial community structures in two carbonate nodules collected from a high methane flux site in a gas hydrate field off the Oki islands in the Sea of Japan. The nodules were formed around sulfate-methane interfaces (SMI) corresponding to 0.7 and 2.2 m below the seafloor. Based on a geochemical analysis, light carbon isotopic values ranging from −54.91‰ to −37.32‰ were found from the nodules collected at the shallow SMI depth, which were attributed to the high contributions of AOM-induced carbonate precipitation. Signatures of methanotrophic archaeal populations within the sedimentary buried nodule were detected based on microbial community composition analyses and quantitative real-time PCR targeted 16S rRNA, and functional genes for AOM. These results suggest that the buried carbonate nodule currently develops AOM-related microbial communities, and grows depending on the continued AOM under high methane flux conditions.

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Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic

Applied and Environmental Microbiology ◽

10.1128/aem.00359-08 ◽

2008 ◽

Vol 74 (22) ◽

pp. 6898-6907 ◽

Cited By ~ 46

Author(s):

Nancy N. Perreault ◽

Charles W. Greer ◽

Dale T. Andersen ◽

Stefanie Tille ◽

Georges Lacrampe-Couloume ◽

...

Keyword(s):

Microbial Community ◽

Heterotrophic Bacteria ◽

Continuous Light ◽

Sulfur Oxidation ◽

Extreme Environment ◽

High Arctic ◽

The Arctic ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Moderate Salinity

ABSTRACT The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy.

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Physicochemical and biological dynamics in a coastal Antarctic lake as it transitions from frozen to open water

Antarctic Science ◽

10.1017/s0954102013000102 ◽

2013 ◽

Vol 25 (5) ◽

pp. 663-675 ◽

Cited By ~ 4

Author(s):

Markus Dieser ◽

Christine M. Foreman ◽

Christopher Jaros ◽

John T. Lisle ◽

Mark Greenwood ◽

...

Keyword(s):

Microbial Community ◽

Physicochemical Parameters ◽

Community Dynamics ◽

Denaturing Gradient Gel Electrophoresis ◽

Microbial Community Composition ◽

Late Summer ◽

Open Water ◽

Rrna Gene ◽

Coastal Lake ◽

16S Rrna Gene Analysis

AbstractPony Lake, at Cape Royds, Antarctica, is a shallow, eutrophic, coastal lake that freezes solid in the winter. Changes in Pony Lake's physicochemical parameters and microbial community were studied during the transition from ice to open water. Due to rising water temperatures, the progressive melt of the ice column and the gradual mixing of basal brines into the remaining water column, Pony Lake evolved physically and chemically over the course of the summer, thereby affecting the microbial community composition. Temperature, pH, conductivity, nutrients and major ion concentrations reached their maximum in January. Pony Lake was colonized by bacteria, viruses, phytoflagellates, ciliates, and a small number of rotifers. Primary and bacterial production were highest in mid-December (2.66 mg C l-1d-1and 30.5 μg C l-1d-1, respectively). A 16S rRNA gene analysis of the bacterioplankton revealed 34 unique sequences dominated by members of theβ- andγ-proteobacterialineages. Cluster analyses on denaturing gradient gel electrophoresis (DGGE) banding patterns and community structure indicated a shift in the dominant members of the microbial community during the transition from winter ice, to early, and late summer lakewater. Our data demonstrate that temporal changes in physicochemical parameters during the summer months determine community dynamics and mediate changes in microbial species composition.

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Evaluating the quorum quenching potential of bacteria associated toAurelia auritaandMnemiopsis leidyi

10.1101/602268 ◽

2019 ◽

Cited By ~ 3

Author(s):

Daniela Prasse ◽

Nancy Weiland-Bräuer ◽

Cornelia Jaspers ◽

Thorsten B.H. Reusch ◽

Ruth A. Schmitz

Keyword(s):

Microbial Community ◽

Marine Invertebrates ◽

Quorum Quenching ◽

Homoserine Lactone ◽

Model Organisms ◽

Mnemiopsis Leidyi ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Ambient Seawater ◽

Moon Jellyfish

AbstractThe associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health and homeostasis of the metaorganism. As one key chemically-mediated interaction, Quorum sensing (QS) and interference with QS among colonizing bacteria ultimately affects the establishment and dynamics of the microbial community on the host. Aiming to address interspecies competition of cultivable microbes associated to merging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi) as well as to evaluate their potential to shape the associated community by interfering with QS, we performed a classical isolation approach. Overall, 84 bacteria were isolated fromA. auritamedusae and polyps, 64 bacteria fromM. leidyi, and 83 bacteria from the ambient seawater, followed by taxonomically classification by full length 16S rRNA gene analysis. The results show that the moon jellyfishA. auritaand the comb jellyM. leidyiharbor a cultivable core microbiota consisting of typical marine and ubiquitously found bacteria (e.g.Chryseobacter, Microbacterium, Micrococcus, Olleya, Phaeobacter, Pseudoalteromonas, Pseudomonas, Rhodococcus, Shewanella, Staphylococcus, andVibrio) which can also be found in the ambient seawater. However, several bacteria were restricted to one host (e.g. forA. aurita: Bacillus, Glaciecola, Ruegeria, Luteococcus;forM. leidyi: Acinetobacter, Aeromonas, Colwellia, Exiguobacterium, Marinomonas, Pseudoclavibacter, Psychrobacter, Sagittula, Thalassomonas) suggesting host-specific microbial community patterns. Evaluating QQ activities, out of 231 isolates, 121 showed QS-interfering activity. They mainly interfered with the acyl homoserine lactone (AHL) based communication, whereas 21 showed simultaneous quorum quenching activities against AHL and autoinducer-2. Overall, this study provides insights into the cultivable part of the microbiota associated to two environmentally important marine non-model organisms and discloses their potential in synthesizing QS interfering compounds, potentially important in shaping a healthy and resilient microbiota.

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Phylogenetic Profiles of In-House Microflora in Drains at a Food Production Facility: Comparison and Biocontrol Implications of Listeria-Positive and -Negative Bacterial Populations

Applied and Environmental Microbiology ◽

10.1128/aem.00468-14 ◽

2014 ◽

Vol 80 (11) ◽

pp. 3369-3374 ◽

Cited By ~ 25

Author(s):

Edward M. Fox ◽

Katie Solomon ◽

John E. Moore ◽

Patrick G. Wall ◽

Séamus Fanning

Keyword(s):

Microbial Community ◽

Food Production ◽

Bacterial Species ◽

Rrna Gene ◽

Production Facility ◽

Production Environment ◽

16S Rrna Gene Analysis ◽

Bacterial Populations ◽

Content Type ◽

Phylogenetic Profiles

ABSTRACTListeriaspecies experience complex interactions with other microorganisms, which may promote growth and colonization of the organism in local environments or negatively affect them. This study investigated the microbial community at a food production facility, examining interactions betweenListeriaand the associated microbiome.Listeriaspecies can be transferred between zones in the production environment by individuals or equipment, and drains may act as a reservoir for the organism, reflecting the microbial flora potentially in the production environment. Drains that were colonized byListeriaspecies and those determined to be free ofListeriawere examined. In each case, 16S rRNA gene analysis was performed using the PhyloChip platform. Some general similarities in bacterial population structure were observed whenListeria-negative and -positive drain communities were compared, with some distinct differences also noted. These included increased populations of the generaPrevotellaandJanthinobacteriumassociated with the absence ofListeriaspecies, whereasEnterococcusandRhodococcuswere in higher abundance in drains colonized byListeriaspecies. Based on these results, a selection of bacterial species were grown in coculture biofilm with aListeria monocytogenesstrain identified as having colonized a drain at the facility. Mixed-species biofilm experiments showed thatJanthinobacteriuminhibited attachment and subsequent biofilm formation ofL. monocytogenes; however,Enterococcus gallinarumsignificantly increased it. The results of this study suggest the microbial community in food processing facilities can impact the colonization ofListeriaspecies and that influencing the microbiome in favor of antilisterial species may reduce the colonization ofListeriaspecies and limit the likelihood of product/process contamination.

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Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

Environments ◽

10.3390/environments8020016 ◽

2021 ◽

Vol 8 (2) ◽

pp. 16

Author(s):

Sergey Kharitonov ◽

Mikhail Semenov ◽

Alexander Sabrekov ◽

Oleg Kotsyurbenko ◽

Alena Zhelezova ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

High Throughput Sequencing ◽

Global Climate ◽

Methane Flux ◽

Molecular Methods ◽

Methane Cycle ◽

Selective Enrichment ◽

Global Climate Changes ◽

Wide Range

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

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