Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

Zhang, Yunhui; Yao, Peng; Sun, Chuang; Li, Sanzhong; Shi, Xiaochong; Zhang, Xiaohua; Liu, Jiwen

doi:10.1111/mec.15937

Cited by 57 publications

(36 citation statements)

References 111 publications

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“…As shown in Figure 1B , DMSP content in the surface sediment of SCS002–SCS011 ranged from 11.25 to 20.90 nmol g –1 (1 and 2 cm), and then reduced rapidly in the top 30 cm, especially between 10 and 30 cm. Our previous study ( Zhang et al, 2021 ) revealed that oxygen was depleted rapidly in the 10-cm sediments, leading to a clear transition in microbial communities. Here, we showed that the DMSP content in sediment decreased dramatically from oxic sediments to anoxic sediments.…”

Section: Resultsmentioning

confidence: 94%

“…As described in our previous study ( Zhang et al, 2021 ), 10 sediment gravity cores were collected on the northern slope of the SCS (18.44–19.26°N, 114.25–115.30°E) ( Figure 1A ), ranging from 6.64 to 8.36 m. The detailed sampling methods and environmental parameters have been reported by Zhang et al (2021) . All 134 sediment samples from 1, 2, 6, 10, 30, 50, 90, 190, 290, 390, 490, 590, 690, and 790 cm depths of these cores have been used to quantify their DMSP content.…”

Section: Methodsmentioning

confidence: 99%

“…The 16S rRNA gene amplicon sequencing of SCS008 (1, 50, 90, 390, and 690 cm) was performed in our previous study ( Zhang et al, 2021 ) and re-analyzed in this study with the enriched samples. The enriched cultures (1 ml) were centrifuged and genomic DNA was extracted from the resulting pellet using the Power Soil DNA Isolation Kit (MoBio Laboratories) and a FastPrep-24 cell disrupter (MP Biomedicals) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

“…The primer set of 515FmodF (5′-GTGYCAGCMGCCGCGGTAA-3′) and 806RmodR (5′-GGACTACNVGGGTWTCTAAT-3′) was used to amplify the V4 hypervariable region of the 16S rRNA gene from bacteria and archaea ( Walters et al, 2016 ). Polymerase chain reactions (PCR), sequencing on an Illumina Miseq PE300 platform (Illumina, San Diego, CA, United States), and quality control of raw reads were performed by the Majorbio Bio-Pharm Technology Co. Ltd. (Majorbio, Shanghai, China) as described by Zhang et al (2021) . Operational taxonomic units (OTUs) were clustered with a 97% similarity cutoff using uparse ( Edgar, 2013 ) (version 7.0.1090 2 ).…”

Section: Methodsmentioning

confidence: 99%

“…However, the DMSP concentration, microbes, and their importance in producing and cycling DMSP in these sediments is unexplored. In a previous study, we obtained 10 sediment cores (6–8 m deep) from the northern slope of the SCS ( Zhang et al, 2021 ), and investigated the vertical profile of microbial abundance and distribution in this region. Here, we quantified the DMSP concentration in the SCS surface and subseafloor sediments, and combined culture-dependent and -independent methods to explore the spatial distribution of DMSP-producing and catabolic bacteria, aiming to reveal (1) the vertical concentration profiles of DMSP in deep-sea sediments, (2) vertical changes of DMSP-producing bacteria groups, and (3) the potential novel DMSP biosynthetic bacteria in the SCS sediments.…”

Section: Introductionmentioning

confidence: 99%

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Dimethylsulfoniopropionate Biosynthetic Bacteria in the Subseafloor Sediments of the South China Sea

Zhang

Sun

et al. 2021

Front. Microbiol.

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Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules, and bacteria in marine sediments have been considered significant producers. However, the vertical profiles of DMSP content and DMSP-producing bacteria in subseafloor sediment have not been described. Here, we used culture-dependent and -independent methods to investigate microbial DMSP production and cycling potential in South China Sea (SCS) sediment. The DMSP content of SCS sediment decreased from 11.25 to 20.90 nmol g–1 in the surface to 0.56–2.08 nmol g–1 in the bottom layers of 8-m-deep subseafloor sediment cores (n = 10). Very few eukaryotic plastid sequences were detected in the sediment, supporting bacteria and not algae as important sediment DMSP producers. Known bacterial DMSP biosynthesis genes (dsyB and mmtN) were only predicted to be in 0.0007–0.0195% of sediment bacteria, but novel DMSP-producing isolates with potentially unknown DMSP synthesis genes and/or pathways were identified in these sediments, including Marinobacter (Gammaproteobacteria) and Erythrobacter (Alphaproteobacteria) sp. The abundance of bacteria with the potential to produce DMSP decreased with sediment depth and was extremely low at 690 cm. Furthermore, distinct DMSP-producing bacterial groups existed in surface and subseafloor sediment samples, and their abundance increased when samples were incubated under conditions known to enrich for DMSP-producing bacteria. Bacterial DMSP catabolic genes were also most abundant in the surface oxic sediments with high DMSP concentrations. This study extends the current knowledge of bacterial DMSP biosynthesis in marine sediments and implies that DMSP biosynthesis is not only confined to the surface oxic sediment zones. It highlights the importance of future work to uncover the DMSP biosynthesis genes/pathways in novel DMSP-producing bacteria.

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Section: Resultsmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Dimethylsulfoniopropionate Biosynthetic Bacteria in the Subseafloor Sediments of the South China Sea

Zhang

Sun

et al. 2021

Front. Microbiol.

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Aerenchyma in emergent plants and rhizospheric microbial communities promote methane fluxes in wetlands

Guo,

Zhang,

et al. 2024

Limnology & Oceanography

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Wetlands are the largest natural source of CH4 globally, yet our understanding of how environmental parameters and microorganisms affect the production and emission of CH4 in emergent plant–sediment systems remains limited. In this study, CH4 fluxes were investigated in a wetland with Canna indica for 42 d, as well as nutrients and microbial community. It was found that the chimney effect formed by aerenchyma in roots, stems, and leaves of C. indica promoted the emission and oxidation of CH4 in the wetland and reduced the CH4 concentration in sediments. Canna indica reduced the nutrient release from surface sediments into the overlying water. Pearson correlation analysis showed that temperature, pH, and oxidation–reduction potential were the main influencing factors for CH4 production and oxidation in the wetland. Canna indica inhibited the diversity of archaeal community but promoted the diversity of bacterial community in the rhizosphere. Stochastic processes had a greater impact on bacterial and archaeal succession trajectories in wetland sediments. Network analysis showed that C. indica promoted interactions among bacteria and archaea that enhanced their ability to resist environmental interference. The well‐developed aerenchyma of C. indica provided an important passage for the transport of CH4 from sediments to the atmosphere and shaped the microbial community structure in the rhizosphere. Meanwhile, CH4 emissions were also constrained by several variables, such as temperature and physiological adaptation in the long term. Thus, it is necessary to plant emergent plants in areas with low CH4 emissions and optimize plant configuration in the context of global warming.

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Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts

Sun,

Zhou,

Cheng

et al. 2023

Microb Ecol

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Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results and phylogenetic beta diversity indices showed that prokaryotic diversity in the sur cial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%) and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also in uence signi cantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in sur cial layers, contrasting with stochastic in uences in deep layers. This was further supported from the detection of a more complex prokaryotic cooccurrence network in the sur cial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions. Sample Collection and Environmental CharacterizationOne sediment core was collected from surface to 26 cm below sea oor (cmbsf) at the Nazimov guyots in Magellan seamount (162.45 °E, 15.18 °N, 5365 m seawater depth) using a four-tube multitube sampler (MC-400, 10×58 cm, Ocean Environmental Sci.&Tech.) during the Dayang 61st-I cruise of P. R. China. Brie y, the sediment core was sliced at 2-cm intervals with a stainless-steel cutter at 13 different sediment intervals (n = 13 samples). A sterile spatula was used to carefully collect sediment from the center of each sediment horizon for DNA extraction to avoid potential contamination. Samples were transferred to sterilized plastic tubes and stored at -80 °C until DNA extraction, and analyses of selected environmental factors like pH, electrical conductivity (EC), available phosphorous (AP), available potassium (AK), available nitrogen (AN), and organic carbon (OC), according to [30,31]. We note that our analyses on AN and AP provide bulk estimations of available N and P in the sediments without further speciation on the contribution of inorganic vs. organic sources. Brie y, samples were air-dried at room temperature in the shade and sieved through a 2-mm screen. The pH an...

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Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

Cited by 57 publications

References 111 publications

Dimethylsulfoniopropionate Biosynthetic Bacteria in the Subseafloor Sediments of the South China Sea

Dimethylsulfoniopropionate Biosynthetic Bacteria in the Subseafloor Sediments of the South China Sea

Aerenchyma in emergent plants and rhizospheric microbial communities promote methane fluxes in wetlands

Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts

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