Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments

Lai, Dengxun; Hedlund, Brian P.; Xie, Wei; Liu, Jingjing; Phelps, Tommy J.; Zhang, Chuanlun; Wang, Peng

doi:10.3389/fmicb.2020.572017

Cited by 5 publications

(5 citation statements)

References 128 publications

(149 reference statements)

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“…ref. 77 ). For simplicity, we omitted the SCS samples in subsequent clustering analysis due to their unusual behavior.…”

Section: Resultsmentioning

confidence: 99%

“…Preprocessing and postprocessing datasets (XLSX) ( 108 ) as well as Jupyter Notebooks (IPYNB) containing Python codes ( 109 ) that were used for data preparation, statistical and unsupervised clustering analyses, and data visualization are deposited at cited Figshare repositories ( 108 , 109 ) and available at https://github.com/PaleoLipidRR/marine-AOA-GDGT-distribution/ or upon request from the corresponding author. Previously published data were used for this work, including GDGTs derived from 1) cultured Thermoproteia ( 39 ), 2) cultured thermophilic AOA ( 40 – 42 ), 3) environmental hot spring samples ( 24 , 43 – 48 ), 4) cultured shallow AOA ( 25 , 28 , 41 ), 5) SPM ( 49 , 50 , 52 , 63 , 66 , 72 , 73 , 77 , 78 , 107 – 111 ), 6) core top sediments ( 62 – 65 , 69 , 72 , 74 , 77 , 78 , 109 , 112 – 115 ), and 7) paleo-marine sediments ( 17 , 21 , 31 – 33 , 51 , 116 …”

Section: Data Availabilitymentioning

confidence: 99%

See 1 more Smart Citation

Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea

Rattanasriampaipong

Zhang

Pearson

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX 86 ) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX 86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline—shallow water samples—also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX 86 . We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today’s deep water marine AOA during the Mesozoic–early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.

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“…ref. 77 ). For simplicity, we omitted the SCS samples in subsequent clustering analysis due to their unusual behavior.…”

Section: Resultsmentioning

confidence: 99%

Section: Data Availabilitymentioning

confidence: 99%

Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea

Rattanasriampaipong

Zhang

Pearson

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…The sedimentation rate in the study area reached 0.77–8.12 cm ka –1 as reported by Schönfeld and Kudrass (1993) and 2–12 cm ka –1 by Shao et al (2001), forming organic‐rich sediment with TOC remaining at a relatively high level (around 1% except for 50 cm) with depth. There was a sudden increase in TOC and change in δ 13 C percentage at 50 cm in most sites, reflecting terrestrial inputs affected by historical climate oscillations such as the glacial and interglacial cycles (Lai et al, 2020; Zhao, Liu, et al, 2017). Distinct TOC, C/N and δ 13 C profiles of SCS005 were observed at 50–490 cm and this may explain the peculiar microbial community compositions in deep sediments of SCS005 featured by large proportions of Actinobacteria, which were considered to be dispersed from different sources of terrestrial input compared with other sites.…”

Section: Discussionmentioning

confidence: 98%

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

et al. 2021

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Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.

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“…Currently, studies in coastal ecosystems have described the taxonomic shifts of microbial communities along salinity gradients, elucidating their functional changes and community assembly mechanisms [27][28][29][30][31]. Fortunato et al conducted a study in a short residence-time estuary connecting the Columbia River using metagenomics and metatranscriptomics.…”

Section: Introductionmentioning

confidence: 99%

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary

Wu,

Li,

et al. 2024

Microbiome

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Background Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the “salt-in” strategy, involving inorganic ion uptake, or the “salt-out” strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem. Results Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline—specific to low-, intermediate-, or high-salinity—based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the “inorganic ion transport and metabolism” COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the “salt-in” strategy, three to the “salt-out” strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K+ transporter related to the “salt-in” strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla. Conclusions We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the “salt-in” strategy mediated by Trk-type K+ transporters for microorganisms thriving under osmotic stress in the short residence-time estuary.

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Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments

Cited by 5 publications

References 128 publications

Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea

Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea

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

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary

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