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Understanding how species interaction and assembly processes structure the abundant and rare bacterial biosphere in soils is crucial for predicting how biodiversity influences ecosystem functioning. Here, we profiled the bacterial communities across a salt marsh ecosystem gradient to investigate the co-occurrence patterns across taxa and the relative influence of ecological processes mediating the assembly of the abundant and rare biospheres in soil. Our results revealed abundant taxa to be ubiquitous across all sample sites, whereas the distributions of the rare taxa were relatively more site-specific. The alpha-diversity indices and beta-diversity of rare sub-communities were significantly higher than those of the abundant sub-communities. Besides, both the taxonomic and functional composition of soil bacterial communities significantly differed between the two biospheres. Furthermore, the influence of stochasticity differed in each sub-community. In particular, stochastic processes were relatively more important in constraining the rare taxa assembly. Co-occurrence network analysis revealed that a few abundant taxa occupy central nodes within the networks, possibly indicating crucial roles as keystone taxa. Collectively, these findings suggest that abundant and rare bacterial biospheres have distinct distributions underpinned by a dynamic interplay of ecological processes and taxa co-occurrence patterns. [ABSTRACT FROM AUTHOR]

Community coalescence is defined as the mixing of intact ecological communities and their environments. It is a common phenomenon in microbial systems with implications for biodiversity, ecosystem functioning, and human health. Research on community coalescence has recently surged, spanning various fields from clinical settings to natural and engineered microbial (eco)systems. We provide a synthesis that integrates an existing framework for invasion biology with commonalities and idiosyncrasies of community coalescence. Embracing the complexity of community coalescence in microbial systems and advancing the study of the ecological processes determining microbial engraftment is of paramount importance to better inform and predict the outcomes of microbiome manipulation across divergent systems. Community coalescence is defined as the mixing of intact ecological communities. From river confluences to fecal microbiota transplantation, community coalescence constitutes a common ecological occurrence affecting natural and engineered microbial systems. In this opinion article, we propose an integrative framework for microbial community coalescence to guide advances in our understanding of this important – yet underexplored – ecological phenomenon. We start by aligning community coalescence with the unified framework of biological invasion and enumerate commonalities and idiosyncrasies between these two analogous processes. Then, we discuss how organismal interactions and cohesive establishment affect coalescence outcomes with direct implications for community functioning. Last, we propose the use of ecological null modeling to study the interplay of ecological processes structuring community reassembly following coalescence. [ABSTRACT FROM AUTHOR]

Chemical nutrient amendment by human activities can lead to environmental impacts contributing to global biodiversity loss. However, the comprehensive understanding of how below- and above-ground biodiversity shifts under fertilization regimes in natural ecosystems remains elusive. Here, we conducted a seven-year field experiment (2011–2017) and examined the effects of different fertilization on plant biodiversity and soil belowground (prokaryotic and eukaryotic) communities in the alpine meadow of the Tibetan Plateau, based on data collected in 2017. Our results indicate that nitrogen addition promoted total plant biomass but reduced the plant species richness. Conversely, phosphorus enrichment did not promote plant biomass and exhibited an unimodal pattern with plant richness. In the belowground realm, distinct responses of soil prokaryotic and eukaryotic communities were observed under fertilizer application. Specifically, soil prokaryotic diversity decreased with nitrogen enrichment, correlating with shifts in soil pH. Similarly, soil eukaryotic diversity decreased with increased phosphorous inputs, aligning with the equilibrium between soil available and total phosphorus. We also established connections between these soil organism communities with above-ground plant richness and biomass. Overall, our study contributes to a better understanding of the sustainable impacts of human-induced nutrient enrichment on the natural environment. Future research should delve deeper into the long-term effects of fertilization on soil health and ecosystem functioning, aiming to achieve a balance between agricultural productivity and environmental conservation. • Soil prokaryotic and eukaryotic diversity decreased under nitrogen and phosphorus fertilization respectively. • Phosphorus fertilizer can alleviate nitrogen fertilizer induced soil acidification and promote soil diversity. • The changes of soil biodiversity were attributed to soil physicochemical characteristics induced by different fertilizer. • Soil prokaryotes and eukaryotes diversity was linked with the plant richness and biomass respectively. [ABSTRACT FROM AUTHOR]

Anthropogenic activities such as long-term fertilizer application are known to lead to losses in above and belowground biodiversity, thereby negatively impacting ecosystem function. However, our understanding of the relative sensitivity of different soil organisms groups to increasing fertilizer application levels remains largely unknown. To address this knowledge gap, we investigated the impacts of different long-term fertilization regimes, and the associated changes in plant communities, on a broad range of soil organisms, including bacteria, fungi, protists, and nematodes, in the alpine meadow ecosystem of the Qinghai-Xizang Plateau. Results showed that the community composition of protists was the most sensitive to different fertilization regimes as compared to those of bacteria, fungi, and nematodes. Changes in the protist community were also most strongly linked to changes in plant richness and biomass under prolonged fertilization. Nitrogen fertilizer addition leads to more deterministic community assembly processes for protist communities, while phosphorus fertilizer application leads to more stochastic assembly processes. Together, our results suggest that protists may be among the most susceptible soil organisms concerning the impact of human disturbances like fertilizer application, highlighting their potential importance as sensitive ecological indicators of human-induced disturbances in terrestrial ecosystems. • Protists was more sensitive to fertilization regimes compared to bacteria, fungi and nematode. • Protists were highly linked to changes in plant richness and biomass. • Nitrogen fertilizer addition led to deterministic processes in protist community assembly. • Phosphorus fertilizer application led to more stochastic assembly processes in protist community assembly. [ABSTRACT FROM AUTHOR]