Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary

Duan, Li; Li, Jialing; Yin, Lingzi; Luo, Xiaoqing; Ahmad, Manzoor; Fang, Bao‐Zhu; Li, Shan-Hui; Deng, Qi-Qi; Wang, Pandeng; Li, Wenjun

doi:10.1016/j.envres.2022.113376

Cited by 19 publications

(6 citation statements)

References 65 publications

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“…The sediment samples were sieved with a 2 mm mesh to remove stones and plant roots before being sealed in sterile plastic bags [24]. The sieved sediment samples were flash-frozen and kept on boards in liquid nitrogen before being stored at −80 • C in the laboratory [25]. Overlying water samples were collected with Van Dorn bottles washed with 10% HCl and stored in triplicate flasks at −4 • C in a cooler [12].…”

Section: Study Area and Samples Collectionmentioning

confidence: 99%

“…After that, the QIIME2 dada2 plugin was used to identify and remove the chimeric sequences [30]. The QIIME2 feature-classifier plugin was then used to align ASV sequences to a pre-trained Greengenes Database 13.8 100% database (trimmed to the V4 region bound by the 515FmodF/806RmodR primer pair) to generate the taxonomy table [25,31,32]. The QIIME2 feature-table plugin filters out any contaminating mitochondrial and chloroplast sequences.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

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The Effect of the Artificial Reef on the Structure and Function of Sediment Bacterial Community

et al. 2022

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The bacterial community in sediment is sensitive to artificial disturbance, and they respond differently to human disturbance, such as changing the nutrient cycling and energy flow in marine ecosystems. However, little is known about the dynamics and distribution of bacterial community structures in marine sediments and potential biogeochemical functions during the long-time succession in marine ranching. In the present study, we compared the dynamics of the bacterial composition and potential biogeochemical functions of sediment to ten years (TR) and one-year new artificial reef (NR) areas using metagenomic next-generation sequencing technology. Results revealed that NR reduces the Pielou’s evenness and Shannon index. Similarly, nonmetric multidimensional scaling showed that the beta diversity of sediment bacterial communities in NR significantly differed between TR and non-artificial reef areas. Previously, TR biomarkers were frequently associated with organic matter decomposing and assimilating in the organically enriched sediments (i.e., Acinetobacter). The soluble reactive phosphate (SRP) and total phosphorus (TP) concentrations were thought to be the primary driving forces in shaping the microbial community in sediment. Pseudomonas, Lactobacillus, and Ralstonia have a significant positive correlation with SRP, TP, nitrate, and TN, but a negative association with pH, Salinity, Hg, and depth. NR was found to have more negative correlation nodes, indicating that taxa face more competition or predation press. Vibrio served as the module-hubs in the network in all areas. In addition, chemoheterotrophy, aerobic chemoheterotrophy, and fermentation were the three most prominent functions of the three areas, accounting for 59.96% of the relative abundance of the functional annotation. Different bacteria in sediments may change the amount of biogeochemical cycle in the marine ranching ecosystem. These findings can increase our understanding of the succession of the microecosystem for the marine ranching sedimentary environment by revealing how artificial reefs affect the indigenous sediment bacterial community and their responses to environmental variation.

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Section: Study Area and Samples Collectionmentioning

confidence: 99%

Section: Bioinformatics Analysismentioning

confidence: 99%

The Effect of the Artificial Reef on the Structure and Function of Sediment Bacterial Community

et al. 2022

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“…Under conditions with varied nutrient sources that many members can metabolize keystone members may be few. However, under conditions with a small number of nutrient sources, especially those that may be energetically expensive to metabolize, keystone members may be more important ( Duan et al, 2022 ). Chitin is one such nutrient source that often promotes interspecies interactions when degraded.…”

Section: Introductionmentioning

confidence: 99%

Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy

et al. 2023

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IntroductionUnderstanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent.MethodsTo characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members.ResultsOur results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration.DiscussionOur findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

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“…Additionally, the loss of biodiversity will first affect the stability of the food web. On the one hand, the loss of redundant structure weakens the network resistance to random interference 9,10 ; on the other hand, with the decline in biodiversity affecting the keystone species in the network, the vulnerability of the network to specific interference has further increased significantly 11 . In summary, the impact of global change on the marine food web is far-reaching, and it is valuable to study the topological properties of the network, which reflect the deep-seated state of complex systems.…”

Section: Introductionmentioning

confidence: 99%

Scale-free characteristics of the global marine food web

Jordán

Zhou

Huo

et al. 2023

Preprint

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The scale-free characteristics of marine food webs reflect the network structural interrelationship, which is ecologically important. Nevertheless, the existence of scale-free networks in marine ecosystems has not been thoroughly discussed. Here, we identify the spatial-temporal pattern of scale-free characteristics and explore the correlation between relevant food web parameters at different scale-free levels. Marine food webs around the globe do not strictly exhibit scale-free characteristics in most regions, and only below 5% of the food webs enter the "strongest fit" level of the scale-free network. We also find food webs in the polar regions indicate relatively high goodness of fit to scale-free networks and state a high latitude dominance hypothesis. The upwelling ecosystem related to ocean currents is prone to form a scale-free web, which exhibits periodic scale-free characteristics. The correlation analysis show that intensified human activities and ocean warming both hinder the formation of food webs with scale-free structures.

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Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary

Cited by 19 publications

References 65 publications

The Effect of the Artificial Reef on the Structure and Function of Sediment Bacterial Community

The Effect of the Artificial Reef on the Structure and Function of Sediment Bacterial Community

Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy

Scale-free characteristics of the global marine food web

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