Frequent Occurrence and Metabolic Versatility of
            <i>Marinifilaceae</i>
            Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas

Li, Jianyang; Dong, Chunming; Lai, Qiliang; Wang, Guangyi; Shao, Zongze

doi:10.1128/msystems.00864-22

Cited by 14 publications

(13 citation statements)

References 86 publications

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“…MnSOD for lignin oxidation was also reported in Marinifilaceae bacteria from the deep sea (Li, Dong, et al, 2022). Its specialization in marine ecosystems may be tentatively interpreted as an adaptation to iron scarcity in the ocean, as marine phytoplankton could increase the synthesis of MnSOD to cope with Fe-limitation (Mamunur Rahman et al, 2014).…”

Section: Distributed Features Of Lignin Degrading Microbial Consortia...mentioning

confidence: 78%

Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Chen,

Lin,

et al. 2024

Molecular Ecology Resources

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Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin‐degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin‐degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter‐connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.

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Section: Distributed Features Of Lignin Degrading Microbial Consortia...mentioning

confidence: 78%

Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Chen,

Lin,

et al. 2024

Molecular Ecology Resources

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“…Isolates from this enrichment were unable to reduce sulfate or nitrate, but rather fermented carbohydrate substrates to H 2 and CO 2 ( Yadav et al, 2020 ). In a different study, metagenome-assembled genomes from the Marinifilaceae subgroup MF-2 enriched during incubations of deep-sea sediment with wood chips contained the genetic repertoire to oxidize lignin to methanol ( Li et al, 2022 ). It thus seems possible that Marinifilaceae could be involved in multiple stages of lignocellulose breakdown, from the saccharification of the full polymer to lignin oxidation and cellulose fermentation.…”

Section: Resultsmentioning

confidence: 99%

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

Frates,

Spietz,

Silverstein

et al. 2023

Front. Microbiol.

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Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.

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“…The microbial community composition in the sulfidic waters of the Black Sea is mostly comprised of uncultivated microbial taxa ubiquitously occurring in anoxic environments worldwide, like Fusobacteriota, Cloacimonadota, Planctomycetota, Chloroflexota, Desulfobacterota, Bacteroidota, and Omnitrophica 6,[11][12][13][14][15][20][21][22][23][24][25] . While some uncultivated clades of the order Clostridiales, Spirochaetota, Fusobacteriota, and Bacteroidota occur in relatively low natural abundance (~1% of the total microbial community), they rapidly respond to OM-rich conditions and become abundant 4,6,13,14 .…”

Section: Resultsmentioning

confidence: 99%

“…Members of the phylum Mycoplasmatota are also present in deep marine habitats and have been identified as specialized degraders of DNA 5,[8][9][10] . In addition to these key taxa, there are also other microbial members affiliated with the phyla Bacteroidota (especially Marinifilaceae, Marinilabiaceae, Lentimicrobiaceae), Desulfobacterota (especially Desulfovibrionaceae, Desulfobacteraceae, Desulfobulbaceae), Planctomycetota (Phycisphaerae), Ignavibacteriota, Chloroflexota (Anaerolineae), Cloacimonadota, and Nanoarchaeota, which have been predicted to be involved in OM degradation in deep marine habitats 4,5,7,[11][12][13][14][15] . Although the identity and potential functions of these microbial taxa are known, their physiology remains largely unknown due to the limited availability of isolated representatives and enrichment cultures.…”

Section: Introductionmentioning

confidence: 99%

Organic matter degradation in the deep, sulfidic waters of the Black Sea: Insights into the ecophysiology of novel anaerobic bacteria

Yadav,

Koenen,

Bale

et al. 2023

Preprint

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Our knowledge about the physiology of deep sea (>1,000 m) microorganisms involved in organic matter (OM) degradation is still scare due to the lack of available isolates, especially from sulfidic environments. In this study, we successfully cultivated and characterized the physiology of a wide range of novel piezotolerant anaerobic bacteria affiliated with the phylaFusobacteriota,Bacillota,Spirochaetota,Bacteroidota,Cloacimonadota,Planctomycetota,MycoplasmatotaandChloroflexotainvolved in OM degradation in deep sulfidic waters of the Black Sea. The novel taxa are specialized in degrading specific types of OM and cover a wide range of physiological categories, including primary degraders, fermenters, and terminal oxidizers. This is the first report which demonstrates this for such a diverse physiological group from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea.

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Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas

Abstract: Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated.

Cited by 14 publications

References 86 publications

Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

Organic matter degradation in the deep, sulfidic waters of the Black Sea: Insights into the ecophysiology of novel anaerobic bacteria

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