Elevated pCO2 alters the interaction patterns and functional potentials of rearing seawater microbiota

Response of microbial communities and biogeochemical cycling functions to sediment physicochemical properties and microplastic pollution under damming and water diversion projects

Understanding the interactions among flow-sediment, microorganisms, and biogeochemical cycles is crucial for comprehending the ecological response mechanisms of dams and water diversion. This study focused on the spatial patterns of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycle functional genes in the water resource for the middle route of the South-to-North Water Diversion Project in China, specifically the Danjiangkou Reservoir (comprising the Han and Dan reservoirs). The investigation incorporated sediment physicochemical properties and microplastic pollution. Numerous microbial species were identified, revealing that microbial communities demonstrated sensitivity to changes in sedimentary mud content. The communities exhibited greater β diversity due to finer sediment particles in the Han Reservoir (HR), whereas in the Dan Reservoir (DR), despite having higher sediment nutrient content and MPs pollution, did not display this pattern. Regarding the composition and structure of microbial communities, the study highlighted that sediment N and P content had a more significant influence compared to particle size and MPs. The quantitative microbial element cycling (QMEC) results confirmed the presence of extensive chemolithotrophic microbes and strong nitrogen cycle activity stemming from long-term water storage and diversion operations. The denitrification intensity in the HR surpassed that of the DR. Notably, near the pre-dam area, biological nitrogen fixation, phosphorus removal, and sulfur reduction exhibited noticeable increases. Dam construction refined sediment, fostering the growth of different biogeochemical cycling bacteria and increasing the abundance of CNPS cycling genes. Furthermore, the presence of MPs exhibited a positive correlation with S cycling genes and a negative correlation with C and N cycling genes. These findings suggest that variations in flow-sediment dynamics and MPs pollution have significant impact the biogeochemical cycle of the reservoir.

Recirculating aquaculture system as microbial community and water quality management strategy in the larviculture of Scylla paramamosain

The structure and function of the water microbial community can change dramatically between different rearing modes. Yet investigations into the relationships between microbial community and water quality remain obscure. We provide the first evidence that rearing modes alter bacterial community and water quality in the rearing water of the mud crab (Scylla paramamosain) larvae. The juveniles in the recirculating aquaculture system (RAS) had a higher viability than those in the water exchange system (WES). RAS had the significantly lower levels of total ammonia nitrogen (TAN), NH3, NO2--N, total nitrogen (TN), total dissolved solids (TDS), and chemical oxygen demand than those of WES. The number of significantly different amplicon sequence variants between rearing modes increased as the larvae developed. NH3, TAN, TDS, NO2--N, and TN were closely related to the late alterations in water bacterial community. Both the FAPROTAX tool and quantitative PCR analysis showed enhanced nitrogen cycling functional potential of water bacterial community of RAS. Random forest analysis identified the enriched water bacteria especially heterotrophic bacteria such as Phaeodactylibacter, Tenacibaculum, and Hydrogenophaga, which were vital in removing nitrogenous compounds via simultaneous nitrification and denitrification. Notably, RAS could save 18.5 m3 of seawater relative to WES in larviculture on the scale of 2.5 m3. Together, these data indicate that RAS could function as microbial community and water quality management strategy in the larviculture of crab.

Adaptive mechanism of the marine bacterium Pseudomonas sihuiensis-BFB-6S towards pCO2 variation: Insights into synthesis of extracellular polymeric substances and physiochemical modulation

Marine bacteria can adapt to various extreme environments by the production of extracellular polymeric substances (EPS). Throughout this investigation, impact of variable pCO2 levels on the metabolic activity and physiochemical modulation in EPS matrix of marine bacterium Pseudomonas sihuiensis - BFB-6S was evaluated using a fluorescence microscope, excitation-emission matrix (EEM), 2D-Fourier transform infrared correlation spectroscopy (2D-ATR-FTIR-COS), FT-NMR and TGA-DSC. From the results at higher pCO2 levels, there was a substantial reduction in EPS production by 58-62.8 % (DW). In addition to the biochemical composition of EPS, reduction in carbohydrates (8.7-47.6 %), protein (7.1-91.5 %), and lipids (16.9-68.6 %) content were observed at higher pCO2 levels. Functional discrepancies of fluorophores (tyrosine and tryptophan-like) in EPS, speckled differently in response to variable pCO2. The 2D-ATR-FTIR-COS analysis revealed functional amides (CN, CC, CO bending, -NH bending in amines) of EPS were preferentially altered, which led to the domination of polysaccharides relevant functional groups at higher pCO2. 1H NMR analysis of EPS confirmed the absence of chemical signals from H-C-COOH of proteins, α, β anomeric protons, and acetyl group relevant region at higher pCO2 levels. These findings can contribute new insights into the influence of pCO2 on the adaptation of marine microbes in future ocean acidification scenarios.

Response of coral bacterial composition and function to water quality variations under anthropogenic influence

Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.

Responses of Fungal Assembly and Co-Occurrence Network of Rhizosphere Soil to Amaranthus palmeri Invasion in Northern China

The interaction between invasive plants and soil microbial communities is critical for plant establishment. However, little is known about the assembly and co-occurrence patterns of fungal communities in the rhizosphere soil of Amaranthus palmeri. The soil fungal communities and co-occurrence networks were investigated in 22 invaded patches and 22 native patches using high-throughput Illumina sequencing. Despite having little effect on alpha diversity, plant invasion significantly altered the composition of the soil fungal community (ANOSIM, p < 0.05). Fungal taxa associated with plant invasion were identified using linear discriminant analysis effect size (LEfSe). In the rhizosphere soil of A. palmeri, Basidiomycota was significantly enriched, while Ascomycota and Glomeromycota were significantly reduced when compared to native plants. At the genus level, the invasion of A. palmeri dramatically increased the abundance of beneficial fungi and potential antagonists such as Dioszegia, Tilletiopsis, Colacogloea, and Chaetomium, while it significantly decreased the abundance of pathogenic fungi such as Alternaria and Phaeosphaeria. Plant invasion reduced the average degree and average path length, and increased the modularity value, resulting in a less complex but more effective and stable network. Our findings improved the knowledge of the soil fungal communities, network co-occurrence patterns, and keystone taxa in A. palmeri-invaded ecosystems.

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Introduction

Plant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.

Methods

Here, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.

Results

As a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.

Discussion

Our study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.