Disentangling protist communities identified from <scp>DNA</scp> and <scp>RNA</scp> surveys in the Pearl River–South China Sea Continuum during the wet and dry seasons

Wu, Wenxue; Liu, Hongbin

doi:10.1111/mec.14867

Cited by 23 publications

(20 citation statements)

References 93 publications

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“…For instance, bacterial communities were generally structured by both niche and neutral processes in Chinese plateau lakes [51], but their specialist and generalist components were structured by contrasting ecological processes [52]. These and many previous studies [8,12,13,48,53] have partitioned beta diversity into components explained by local and regional factors. Regional factors are represented by spatial distance, an approach which is often compounded by the fact that distance effect is most likely overestimated, since it cannot exclude the impacts of unmeasured environmental variables [14].…”

Section: Discussionsupporting

confidence: 51%

Community Assembly Mechanisms Underlying the Core and Random Bacterioplankton and Microeukaryotes in a River–Reservoir System

Isabwe

Ren

Wang

et al. 2019

Water

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Whether bacterioplankton are assembled in the same way as microeukaryotes is a key question that has been answered only partially in microbial ecology. In particular, relating distribution patterns to the underlying ecological processes for plankton communities in highly dynamic ecosystems, such as river–reservoirs subjected to anthropogenic impacts, remains largely unstudied. Here, we analyzed taxonomic distribution patterns, and unraveled community assembly processes underlying the core and random bacterioplankton and microeukaryotes from a subtropical river–reservoir system. These plankton domains were modelled using the spatial abundance distributions (SpADs) of the operational taxonomic units (OTUs) as a proxy for abundant and rare taxa delineation. Both bacterioplankton and microeukaryote plankton communities exhibited significant distance–decay relationships, and samples were grouped depending on reservoir or river habitats. The neutral community model showed that 35–45% of the plankton community variation could be explained by neutral processes. The phylogenetic null model revealed that dispersal limitation accounted for the largest percentage of pairwise comparisons (42–68%), followed by environmental selection (18–25%). We concluded that similar prevalence of ecological processes acting on particular subsets of the bacterioplankton and microeukaryotes might have resulted from similar responses to environmental change, potentially induced by human activities in the watershed.

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Section: Discussionsupporting

confidence: 51%

Community Assembly Mechanisms Underlying the Core and Random Bacterioplankton and Microeukaryotes in a River–Reservoir System

Isabwe

Ren

Wang

et al. 2019

Water

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“…In contrast, high-throughput sequencing technologies focusing on RNA can be used to evaluate relative metabolic activities due to RNA relatedness to enzyme production and their sensitivity to environmental changes (Charvet et al, 2014;Pawlowski et al, 2014). Several studies have successfully determined the microbial composition in the water column of the SCS using both DNA and RNA investigations (Xu et al, 2017;Wu and Liu, 2018). However, the survey of sedimentary microbial communities conducted by employing DNA and RNA molecules is currently lacking, especially in SCS cold seep unities.…”

Section: Introductionmentioning

confidence: 99%

Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea

et al. 2020

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Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.

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“…However, the varied RNA: DNA ratios of taxonomic groups among samples should be interpreted cautiously, because the presence of rRNA indicates the possible ribosomal activity and the potential of protein synthesis, instead of providing an indicator of cell activity (Blazewicz et al, 2013). Confined to a specific group, Wu and Liu (2018) found the relative metabolic activities of Bacillariophyceae species in Pearl River-South China Sea Continuum were significantly affected by the PO 4 concentration and salinity. In order to obtain continuous relationship of the relative metabolic activities of individual OTUs in our samples, we selected OTUs only occurred in both DNA and RNA surveys (Hu et al, 2016) and appeared in all samples within Mamiellophyceae, Pelagophyceae, and Spirotrichea for the further metabolic activities analyses.…”

Section: Discussionmentioning

confidence: 99%

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Wang

Xie

et al. 2019

Front. Microbiol.

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Picoeukaryotes play an important role in the biogenic element cycle and energy flow in oligotrophic ecosystems. However, their biodiversity and activity are poorly studied in open ocean systems, such as the northwestern Pacific Ocean, which is characterized by a complex hydrological setting. Here, we investigated the diversity and activity of picoeukaryotes in the northwestern Pacific Ocean using high-throughput sequencing targeting the V9 region of 18S rDNA and rRNA. Our results showed that the DNA picoeukaryotic communities were mainly represented by Mamiellophyceae, MAST, MALV-II, Spirotrichea, Prymnesiophyceae, and MALV-I (69.33% of the total DNA reads), and the RNA communities were dominated by Spirotrichea, Mamiellophyceae, MAST, Pelagophyceae, and MALV-II (67.46% of the total RNA reads). The number of operational taxonomic units (OTUs) was significantly affected by temperature and salinity, and was decreased with the increasing nutrient concentration both in the DNA and RNA surveys. Significant differences were observed in the community composition between DNA-based and RNA-based molecular approaches, and these differences were mainly attributed to Mamiellophyceae, Spirotrichea, and Pelagophyceae. The RNA: DNA ratio was used as a proxy for relative metabolic activity of the individual OTUs. We found that the relative metabolic activities of Mamiellophyceae, Spirotrichea, and Pelagophyceae species in the northwestern Pacific Ocean were highly affected by the nutrient concentration, i.e., the NO3 + NO2 and SiO3 concentration. Overall, our study shed light on picoeukaryotic diversity and distribution in the northwestern Pacific Ocean and revealed the correlation between the diversity, relative metabolic activities of marine picoeukaryotes, and the environmental factors.

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Disentangling protist communities identified from DNA and RNA surveys in the Pearl River–South China Sea Continuum during the wet and dry seasons

Cited by 23 publications

References 93 publications

Community Assembly Mechanisms Underlying the Core and Random Bacterioplankton and Microeukaryotes in a River–Reservoir System

Community Assembly Mechanisms Underlying the Core and Random Bacterioplankton and Microeukaryotes in a River–Reservoir System

Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

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