Environmental microbiome 

About: Environmental microbiome is an academic journal published by Springer Nature. The journal publishes majorly in the area(s): Biology & Medicine. It has an ISSN identifier of 2524-6372. It is also open access. Over the lifetime, 147 publications have been published receiving 428 citations.

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Abstract: Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Abstract: Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.

Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies

Abstract: It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.

Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies

Abstract: It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.

Distribution of soil viruses across China and their potential role in phosphorous metabolism

Abstract: Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China.Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils.The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.