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  • Peng, Yisheng  (5)
  • Tu, Qichao  (5)
  • 1
    Online Resource
    Online Resource
    Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes
    Wiley ; 2023
    In:  mLife Vol. 2, No. 3 ( 2023-09), p. 253-266
    Details
    In: mLife, Wiley, Vol. 2, No. 3 ( 2023-09), p. 253-266
    Abstract: Understanding the adaptation of microbial communities to changing environments is a critical issue in microbial ecology and evolution, especially reflected in the change of microbial genome sizes and their functional capability of biogeochemical cycles. In this study, we analyzed rhizosphere microbiomes from native and introduced mangrove species and found that the introduced mangrove rhizosphere microbiome tended to adapt to a new or changing environment by recruiting more genetic elements, resulting in a higher average genome size but lower functional potentials of CH 4 cycling, N 2 fixation, and inorganic S cycling. Our results revealed the potential mechanism of how native soil microbiomes adapted to the introduced mangrove rhizosphere, advancing our understanding of mangrove rhizosphere microbiomes.
    Type of Medium: Online Resource
    ISSN: 2097-1699 , 2770-100X
    URL: Issue
    URL: Article
    DOI: 10.1002/mlf2.v2.3
    DOI: 10.1002/mlf2.12077
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 3120417-X
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  • 2
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    Online Resource
    Chemoautotrophic sulphur oxidizers dominate microbial necromass carbon formation in coastal blue carbon ecosystems
    Wiley ; 2023
    In:  Functional Ecology Vol. 37, No. 10 ( 2023-10), p. 2634-2651
    Details
    In: Functional Ecology, Wiley, Vol. 37, No. 10 ( 2023-10), p. 2634-2651
    Abstract: Coastal blue carbon (C) ecosystems are recognized as efficient natural C sinks and play key roles in mitigating global climate change. Microbially driven C, nitrogen (N) and sulphur (S) cycles are crucial for ecosystem functioning, but how microorganisms drive C sink formation and C sequestration in coastal sediments remains unclear. In this study, we conducted a comprehensive analysis of amino sugars, C, N and S cycling genes/pathways and their associated taxa in coastal sediments of native ( Cyperus malaccensis and Kandelia obovata ) and alien ( Spartina alterniflora and Sonneratia apetala ) vegetation. Compared to the alien‐vegetated coastal sediment, the native‐vegetated coastal sediment had significantly ( p   〈  0.05) higher microbial necromass C and higher functional potentials of chemoautotrophic C fixation, C degradation, methane cycling, N 2 fixation, S oxidation and sulphate reduction. Also, our analysis of coastal sediment microbiomes showed that S oxidation could be coupled with C fixation and/or nitrate/nitrite reduction. S oxidation, C degradation and C fixation were found to be key functional pathways for predicting sediment microbial necromass C. Additionally, the sulphur‐oxidizing Burkholderiales metagenome‐assembled genomes (MAGs) were a key functional group that dominated chemoautotrophic C fixation in coastal sediments. These results suggested that chemoautotrophic S oxidizers, in particular Burkholderiales with a novel lineage, might be the key microbial group that dominates microbial necromass C formation in coastal sediments through microbial anabolism (C fixation);the coupling of microbially driven C, N and S cycling processes; and the deposition of microbially derived C. This study provides novel insights into the importance of chemoautotrophic S oxidizers for microbial necromass formation and shed new light on the microbial mechanism of C sink formation in coastal ecosystems, which also has important implications for enhancing C sequestration in coastal wetlands. Read the free Plain Language Summary for this article on the Journal blog.
    Type of Medium: Online Resource
    ISSN: 0269-8463 , 1365-2435
    URL: Issue
    URL: Article
    DOI: 10.1111/fec.v37.10
    DOI: 10.1111/1365-2435.14417
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2020307-X
    detail.hit.zdb_id: 619313-4
    SSG: 12
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  • 3
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    Online Resource
    MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes
    Wiley ; 2022
    In:  Molecular Ecology Resources Vol. 22, No. 5 ( 2022-07), p. 1803-1823
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 22, No. 5 ( 2022-07), p. 1803-1823
    Abstract: Methane is a critical greenhouse gas with significant impacts on environmental and global change. However, CH 4 cycling processes and coupling mechanisms with the biogeochemical cycling of carbon, nitrogen, sulfur and metals in the environment remain elusive. To fill such knowledge gaps, we constructed a manually curated methane cycling database (MCycDB) for comprehensive and accurate analysis of methane cycling microbial communities. MCycDB contains 298 methane cycling gene families covering 10 methane metabolism pathways with 610,208 representative sequences, and associated reference sequences from the NCBI RefSeq database with 48 phyla and 2,197 genera, and five phyla and 100 genera for bacteria and archaea, respectively. Also, homologous groups from public orthology databases were identified and included in MCycDB to reduce false positive assignments. We applied MCycDB to profile methane cycling gene families and associated taxonomic groups from various environments. Gene families involved in methanogenesis were abundant in hot spring sediment and less abundant in freshwater, whereas the ones involved in aerobic oxidation of methane were abundant in permafrost and peatland. This study demonstrates that MCycDB is a useful tool for studying microbially‐driven methane cycling processes with high specificity, coverage and accuracy.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v22.5
    DOI: 10.1111/1755-0998.13589
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2406833-0
    detail.hit.zdb_id: 2406816-0
    SSG: 12
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  • 4
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    SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways
    Wiley ; 2021
    In:  Molecular Ecology Resources Vol. 21, No. 3 ( 2021-04), p. 924-940
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 21, No. 3 ( 2021-04), p. 924-940
    Abstract: Microorganisms play important roles in the biogeochemical cycling of sulphur (S), an essential element in the Earth's biosphere. Shotgun metagenome sequencing has opened a new avenue to advance our understanding of S cycling microbial communities. However, accurate metagenomic profiling of S cycling microbial communities remains technically challenging, mainly due to low coverage and inaccurate definition of S cycling gene families in public orthology databases. Here we developed a manually curated S cycling database (SCycDB) to profile S cycling functional genes and taxonomic groups for shotgun metagenomes. The developed SCycDB contains 207 gene families and 585,055 representative sequences affiliated with 52 phyla and 2684 genera of bacteria/archaea, and 20,761 homologous orthology groups were also included to reduce false positive sequence assignments. SCycDB was applied for functional and taxonomic analysis of S cycling microbial communities from four habitats (freshwater, hot spring, marine sediment and soil). Gene families and microorganisms involved in S reduction were abundant in the marine sediment, while those of S oxidation and dimethylsulphoniopropionate transformation were abundant in the soil. SCycDB is expected to be a useful tool for fast and accurate metagenomic analysis of S cycling microbial communities in the environment.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v21.3
    DOI: 10.1111/1755-0998.13306
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2406833-0
    detail.hit.zdb_id: 2406816-0
    SSG: 12
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  • 5
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    Online Resource
    Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes
    Springer Science and Business Media LLC ; 2023
    In:  Microbiome Vol. 11, No. 1 ( 2023-04-05)
    Details
    In: Microbiome, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2023-04-05)
    Abstract: Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH 4 ), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. Results Our results showed that the metabolic pathways involved in CH 4 , N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly ( P 〈 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0–15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N 2 O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly ( P 〈 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH 4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. Conclusions In addition to offering a perspective on the vertical distribution of microbially driven CH 4 , N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N 2 O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change.
    Type of Medium: Online Resource
    ISSN: 2049-2618
    URL: Article
    DOI: 10.1186/s40168-023-01501-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2697425-3
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