Microbial functional assemblages predicted by the FAPROTAX analysis are impacted by physicochemical properties, but C, N and S cycling genes are not in mangrove soil in the Beibu Gulf, China

Yang, Zicong; Peng, Chunyan; Cao, Hongming; Jin, Zhen; Gong, Bin; Li, Lü; Wang, Lin; He, Yu; Ling, Meng; Lin, Juncheng; Lu, Liulin

doi:10.1016/j.ecolind.2022.108887

Cited by 47 publications

(19 citation statements)

References 71 publications

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“…Interestingly, unlike the FAPROTAX results, the PICRUST2 results suggest that OA would not affect these biological pathways (e.g., cellular respiration, nitrogen metabolism, sulfur metabolism) of prokaryotes in intertidal soft sediments. These conflicting findings can mostly be attributed to the different characteristics of the two prediction tools, i.e., FAPROTAX annotates functions based on published metabolic and ecological functions, while PICRUST2 predicts metagenomic functions based on an arbitrary OTU/ASV table (Liu et al, 2020;Yang et al, 2022). Based on previous research, FAPROTAX works especially well in predicting ecologically relevant functions (e.g., biogeochemical cycles) of marine microbes (Louca et al, 2016;Sansupa et al, 2021).…”

Section: Functional Predictionmentioning

confidence: 99%

Ocean acidification alters the benthic biofilm communities in intertidal soft sediments

et al. 2023

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Microphytobenthos (MPB) and bacterial biofilms play crucial roles in primary and secondary production, nutrient cycling and invertebrate settlement in coastal ecosystems, yet little is known of the effects of ocean acidification (OA) on these communities in intertidal soft sediments. To fill in this gap, a 28-day CO2 enhancement experiment was conducted for the benthic biofilms in soft intertidal sediments (muds and sands) from Qingdao, China. This experiment included three CO2 treatments: 400 ppm CO2 (control), 700 ppm CO2 and 1000 ppm CO2 (IPCC predicted value in 2100), which were established in a three-level CO2 incubator that can adjust the CO2 concentration in the overlying air. The effects of OA on benthic biofilms were assessed in the following three aspects: MPB biomass, biofilm community structure and microbial biogeochemical cycling (e.g., C-cycle, N-cycle and S-cycle). This study found that the 700 ppm CO2 treatment did not significantly affect the benthic biofilms in intertidal soft sediments, but the 1000 ppm CO2 treatment significantly altered the biofilm community composition and potentially their role in microbial biogeochemical cyc\ling in sediments (especially in sandy sediments). For the bacterial community in biofilms, the 1000 ppm CO2 enhancement increased the relative abundance of Alteromonadales and Bacillales but decreased the relative abundance of Rhodobacterales and Flavobacteriales. For microbial biogeochemical cycling, the 1000 ppm CO2 treatment enhanced the potential of chemoheterotrophic activity, nitrate reduction and sulfur respiration in sediments, likely resulting in a more stressful environment (hypoxic and enriched H2S) for most benthic organisms. Even though incubations in this study were only 28 days long and thus couldn’t fully accommodate the range of longer-term adaptions, it still suggests that benthic biofilms in intertidal sandy sediments are likely to change significantly near the end of the century if anthropogenic CO2 emissions unmitigated, with profound implications on local ecosystems and biogeochemical cycling.

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Section: Functional Predictionmentioning

confidence: 99%

Ocean acidification alters the benthic biofilm communities in intertidal soft sediments

et al. 2023

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“…Functional differences in the rhizosphere bacterial community of weedy rice, cultivated rice and cultivated rice surrounded by weedy rice FAPROTAX is a manually constructed database for predicting the function of bacteria and archaea in terrestrial and marine ecosystems [57]. A number of studies have used FAPROTAX to predict and analyse the diversity and function of soil bacteria in different environments and thus to analyse some of the environmental factors that determine functional microbial communities in soils [58,59]. Iron plays an important role in biochemistry in natural environments [60,61].…”

Section: Key Microbial Species In Co-occurrence Network May Lead To A...mentioning

confidence: 99%

The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil

Sun

et al. 2022

BMC Microbiol

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Background Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study. Results In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice. Conclusions Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils.

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“…Recently, several tools have been developed for the prediction of functional gene content of microbial communities based on only taxonomic composition from metabarcoding data (Gavin et al., 2020; Wemheuer et al., 2020; Yang et al., 2022). Another option for high throughput functional community profiling is the use of microarrays.…”

Section: Introductionmentioning

confidence: 99%

Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches

Abad‐Recio,

Alonso‐Sáez,

Lanzén

2024

Environmental DNA

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Coastal environments, crucial and intricate ecosystems, face threats from human activities like pollution, eutrophication, and climate change. Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics. Results revealed significant functional diversity across all sampling sites, irrespective of their environmental status. Most predicted KEGG Orthologs (KOs) showed consistency between metagenomics and Tax4Fun datasets, with correlated abundances. However, abundances derived from GeoChip did not correlate with either dataset. When comparing estuaries based on environmental status, Tax4Fun and metagenomics identified over 24% of KOs with significantly different abundances. KOs overrepresented in estuaries with a poor ecological status displayed an abundance of pathways associated with anaerobic metabolism, such as methanogenesis.

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Microbial functional assemblages predicted by the FAPROTAX analysis are impacted by physicochemical properties, but C, N and S cycling genes are not in mangrove soil in the Beibu Gulf, China

Cited by 47 publications

References 71 publications

Ocean acidification alters the benthic biofilm communities in intertidal soft sediments

Ocean acidification alters the benthic biofilm communities in intertidal soft sediments

The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil

Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches

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