Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments

Behera, Pratiksha; Mohapatra, Madhusmita Mohanty; Kim, Ji Yoon; Rastogi, Gurdeep

doi:10.1016/j.scitotenv.2019.135709

Cited by 26 publications

(7 citation statements)

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“…Salinity has been considered as a stress factor of bacteria community and can affect bacteria respiratory activity, membrance polarization and integrity, and DNA and RNA contents [ 48 , 49 ]; therefore, salinity has been reported to be a major determinant affecting the biogeographic pattern of bacterial communities across lake and marine ecosystems [ 50 ]. For planktonic archaea, although Crenarchaeota, Euryarchaeota and Thaumarchaeota are well known as the dominant archaea in brackish and pond sediment [ 51 , 52 ], Nanoarchaeaeota are the top one in this study (Fig. 3 ), indicating their pervasiveness in the coastal wetland waters.…”

Section: Discussionmentioning

confidence: 79%

Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China’s coastal wetlands

Wang

Liu

Yang

et al. 2021

Environmental Microbiome

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Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China’s coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former’s community structure, whereas stochastic processes regulate the latter’s, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.

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Section: Discussionmentioning

confidence: 79%

Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China’s coastal wetlands

Wang

Liu

Yang

et al. 2021

Environmental Microbiome

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“…Coastal ecosystems store large amounts of blue carbon due to their high primary productivity rates and slow decomposition rates (Donato et al, 2011;McLeod et al, 2011;Alongi, 2014). Meanwhile, coastal ecosystems exhibit special environmental conditions such as high salinity, aerobic-anaerobic exchange, and rich organic matter, supporting that various unique microbes for biogeochemical cycling of carbon, nitrogen and sulfur (Lin et al, 2019;Zhang C. J. et al, 2019Zhang C. J. et al, , 2020Behera et al, 2020;Li et al, 2021). Previous studies indicated that the diversity, assembly and functional traits of microbial communities varied across coastal ecosystems (Lauber et al, 2009;Rousk et al, 2010;Rath and Rousk, 2015;Ma et al, 2017;Zhong et al, 2017;Yu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Environmental Filtering by pH and Salinity Jointly Drives Prokaryotic Community Assembly in Coastal Wetland Sediments

et al. 2022

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Understanding the microbial community assembly is an essential topic in microbial ecology. Coastal wetlands are an important blue carbon sink, where microbes play a key role in biogeochemical cycling of nutrients and energy transformation. However, the drivers controlling the distribution patterns and assembly of bacterial and archaeal communities in coastal wetland are unclear. Here we examined the diversity, co-occurrence network, assembly processes and environmental drivers of bacterial and archaeal communities from inshore to offshore sediments by the sequencing of 16S rRNA gene amplicons. The value of α- and β-diversity of bacterial and archaeal communities generally did not change significantly (P > 0.05) between offshore sites, but changed significantly (P < 0.05) among inshore sites. Sediment pH and salinity showed significant effects on the diversity and keystone taxa of bacterial and archaeal communities. The bacterial and archaeal co-occurrence networks were inextricably linked with pH and salinity to formed the large network nodes, suggesting that they were the key factors to drive the prokaryotic community. We also identified that heterogeneous and homogeneous selection drove the bacterial and archaeal community assembly, while the two selections became weaker from offshore sites to inshore sites, suggesting that deterministic processes were more important in offshore sites. Overall, these results suggested that the environmental filtering of pH and salinity jointly governed the assembly of prokaryotic community in offshore sediments. This study advances our understanding of microbial community assembly in coastal wetland ecosystems.

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“…As expected from anaerobic microbes, archaea are virtually absent from surface samples (less than 6/10.000 for C, D, and 4/1000 for E). In the sample where they are in sizable amounts, the archaeal population is dominated by Bathyarcheota (a recently described clade of methanogens belonging to the TACK phylum) (56), Nitrososphaeria (a class of chemolithoautotrophic ammonia oxidizing archaea belonging to Thaumarchaea phylum and exhibiting global distribution in soils) (57), and Methanomicrobia (a class of methanogens belonging to the Euryarchaeota and previously noticed to be enriched in macrophytes rhizosphere sediments) (58).…”

Section: Resultsmentioning

confidence: 99%

High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

Rigou

Christo-Foroux

Santini

et al. 2021

Preprint

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SummaryBackgroundAntimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum β-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earth’s climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost.MethodsEnvironmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including nine permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified β-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes.FindingsA total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different β-lactamases from class A to D were identified.InterpretationNo clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of β-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost.FundingCNRS PRC research grant (PRC1484-2018) to C.A. E C-F was supported by a PhD grant (DGA/DS/MRIS) #2017 60 0004. GG and JS were funded by ERC PETA-CARB (#338335) and the HGF Impulse and Networking Fund (ERC-0013).

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Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments

Cited by 26 publications

References 67 publications

Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China’s coastal wetlands

Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China’s coastal wetlands

Environmental Filtering by pH and Salinity Jointly Drives Prokaryotic Community Assembly in Coastal Wetland Sediments

High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

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