Local biotic interactions drive species-specific divergence in soil bacterial communities

Assembly mechanisms, not species pool, shape β-diversity of soil methanotrophic communities in steppes of China

Introduction

One of the central aims in ecology is elucidating the mechanisms that shape community diversity. While biodiversity patterns across geographical gradients are often attributed both to local assembly processes and regional species pools, the distinct roles of these factors in shaping soil aerobic methanotrophic diversity remain underexplored.

Methods

Using amplicon sequencing and bioinformatics analysis, this study focuses on comparing the relative importance of species pool and community assembly processes in shaping soil methanotrophic communities across three distinct plateaus in China: the Loess Plateau, the Qinghai-Tibetan Plateau, and the Inner Mongolian Plateau. Each of these plateaus includes three distinct steppe habitats: desert, meadow, and typical steppe.

Results

Our findings reveal that pmoA beta (β)-diversity followed a distance-decay pattern, which declined with geographical distance at different rates depending on the steppe type and area, potentially due to diverse mechanisms of community assembly. Moreover, a decoupling between β-diversity and gamma-diversity observed, suggesting that local community assembly mechanisms primarily account for variations in β-diversity patterns. Furthermore, the relative significance of these assembly processes (e.g., dispersal limitation, drift, environmental filtering, and biotic interactions) varies according to spatial scales and steppe types. Notably, the differential environmental conditions (such as soil pH, yearly average temperature, and precipitation) across scales and steppe habitats primarily modulate the intensity of these assembly processes, thereby influencing β-diversity.

Conclusion

In summary, our study emphasizes the crucial role of local community assembly in changing soil methanotrophic β-diversity's geographical patterns, highlighting the significance of a nuanced understanding of these processes for effective conservation and management strategies.

Immigration reduces selection in water microbial community assembly

To investigate the influence of immigration on the selection in structuring local water bacterial communities, we conducted a new community assembly experiment using microcosms filled with sterile original water medium under outdoor conditions. We collected air particulate matter from dust pooled from samples collected at 10 locations across ~20 km in a warm temperate region in Linfen City (northern China). The immigration rates were increased by introducing air particulate matter into the microcosms. The diversity, structure, and composition of the bacterial community in the water were assessed using 16S rRNA gene amplicon sequencing on the 13th and 60th days after the start of the experiment. Our results showed that increasing immigration did not lead to significant changes in the overall diversity of the total bacterial community on the 13th day. However, on the 60th day, diversity significantly increased. The variation explained by the environment substantially decreased from the 13th to the 60th day. The amount decreased from the control to the high immigration treatments, with a range of 65.0 to 29.8% on the 13th day and 34.0 to 15.4% on the 60th day. The dominant phyla differed significantly. In the early stage, Proteobacteria (69.6%) accounted for a higher relative average abundance, while Firmicutes (4.6%), Cyanobacteria (6.0%), Planctomycetota (8.1%), Verrucomicrobiota (2.0%), and Halobacterota (0.9%) were more abundant in the late stage. Additionally, the late stage had an average of 33 phyla, compared to 15 phyla in the early stage. All the results suggested a minimal role of dispersal limitation in structuring water bacterial communities in the early stage, whereas, in the late stage, the bacterial communities might experience dispersal swamping in our study area. Variance partitioning indicated that throughout the experiment, increasing immigration weakened the signal of environmental selection in the water microbial community assembly. These results expand our understanding of the impact of immigration on environmental selection and provide insights into the varying importance of dispersal and selection on microbial community assembly at different stages of succession.

Exploring interspecific interaction variability in microbiota: A review

Interspecific interactions are an important component and a strong selective force in microbial communities. Over the past few decades, there has been a growing awareness of the variability in microbial interactions, and various studies are already unraveling the inner working dynamics in microbial communities. This has prompted scientists to develop novel techniques for characterizing the varying interspecific interactions among microbes. Here, we review the precise definitions of pairwise and high-order interactions, summarize the key concepts related to interaction variability, and discuss the strengths and weaknesses of emerging characterization techniques. Specifically, we found that most methods can accurately predict or provide direct information about microbial pairwise interactions. However, some of these methods inevitably mask the underlying high-order interactions in the microbial community. Making reasonable assumptions and choosing a characterization method to explore varying microbial interactions should allow us to better understand and engineer dynamic microbial systems.

Enhancing mango yield and soil health with organic and slow-release fertilizers: A multifaceted evaluation

Excessive utilization of chemical fertilizers in mango orchards not only hampers the attainment of sustainable harvests but also poses significant ecological detriments. This investigation proposes a promising solution by advocating the judicious replacement of chemical fertilizers with organic fertilizer (OF) and slow-release fertilizer (SRF), with potential to bolster soil health and augment crop productivity. In light of the promise held by these alternatives, it is imperative to establish detailed fertilization protocols for enhanced sustainable practices in mango farming. This two-year field study employed a comprehensive suite of seven fertilization strategies, unveiling that a 25 % chemical fertilizers substitution with OF and SRF improved mango yields by 12.5 % and 11.3 %, respectively, over standard practices. Additionally, these approaches substantially augmented the nutritional quality of mangoes, evident from Vitamin C enhancements of 53.9 % to 56.9 %, and improvements in sugar-to-acid ratio (19.2 %-30.3 %) and solid-to-acid ratio (12.1 %-25.3 %). Notably, the application of OF and SRF led to increased leaf nitrogen and phosphorus concentrations, while simultaneously reducing soil phosphorus and potassium levels. Furthermore, these fertilizers fostered the growth of beneficial soil microorganisms, namely Actinobacteria and Proteobacteria, and strengthened the synergy within the soil bacterial community, hence optimizing bacterial competition and nutrient cycling. The study proposes that the adoption of OF or SRF can effectively regulate soil nutrient balance, promote resilient and functional soil bacterial ecosystems, and ultimately improve mango yield and fruit quality. It recommends a fertilization scheme incorporating 25 % organic or slow-release nitrogen to align with ecological sustainability goals, promoting a more vigorous and resilient soil and crop system.

Consistent community assembly but contingent species pool effects drive β-diversity patterns of multiple microbial groups in desert biocrust systems

One of the key goals of ecology is to understand how communities are assembled. The species co-existence theory suggests that community β-diversity is influenced by species pool and community assembly processes, such as environmental filtering, dispersal events, ecological drift and biotic interactions. However, it remains unclear whether there are similar β-diversity patterns among different soil microbial groups and whether all these mechanisms play significant roles in mediating β-diversity patterns. By conducting a broad survey across Chinese deserts, we aimed to address these questions by investing biological soil crusts (biocrusts). Through amplicon-sequencing, we acquired β-diversity data for multiple microbial groups, that is, soil total bacteria, diazotrophs, phoD-harbouring taxa, and fungi. Our results have shown varying distance decay rates of β-diversity across microbial groups, with soil total bacteria showing a weaker distance-decay relationship than other groups. The impact of the species pool on community β-diversity varied across microbial groups, with soil total bacteria and diazotrophs being significantly influenced. While the contributions of specific assembly processes to community β-diversity patterns varied among different microbial groups, significant effects of local community assembly processes on β-diversity patterns were consistently observed across all groups. Homogenous selection and dispersal limitation emerged as crucial processes for all groups. Precipitation and soil C:P were the key factors mediating β-diversity for all groups. This study has substantially advanced our understanding of how the communities of multiple microbial groups are structured in desert biocrust systems.

Effect of aridity on the β-diversity of alpine soil potential diazotrophs: insights into community assembly and co-occurrence patterns

Microbial diversity plays a vital role in the maintenance of ecosystem functions. However, the current understanding of mechanisms that shape microbial diversity along environmental gradients at broad spatial scales is relatively limited, especially for specific functional groups, such as potential diazotrophs. Here, we conducted an aridity-gradient transect survey from 60 sites across the Tibetan Plateau, the largest alpine ecosystem of the planet, to investigate the ecological processes (e.g., local species pools, community assembly processes, and co-occurrence patterns) that underlie the β-diversity of alpine soil potential diazotrophic communities. We found that aridity strongly and negatively affected the abundance, richness, and β-diversity of soil diazotrophs. Diazotrophs displayed a distance-decay pattern along the aridity gradient, with organisms living in lower aridity habitats having a stronger distance-decay pattern. Arid habitats had lower co-occurrence complexity, including the number of edges and vertices, the average degree, and the number of keystone taxa, as compared with humid habitats. Local species pools explained limited variations in potential diazotrophic β-diversity. In contrast, co-occurrence patterns and stochastic processes (e.g., dispersal limitation and ecological drift) played a significant role in regulating potential diazotrophic β-diversity. The relative importance of stochastic processes and co-occurrence patterns changed with increasing aridity, with stochastic processes weakening whereas that of co-occurrence patterns enhancing. The genera Geobacter and Paenibacillus were identified as keystone taxa of co-occurrence patterns that are associated with β-diversity. In summary, aridity affects the co-occurrence patterns and community assembly by regulating soil and vegetation characteristics and ultimately shapes the β-diversity of potential diazotrophs. These findings highlight the importance of co-occurrence patterns in structuring microbial diversity and advance the current understanding of mechanisms that drive belowground communities.IMPORTANCERecent studies have shown that community assembly processes and species pools are the main drivers of β-diversity in grassland microbial communities. However, co-occurrence patterns can also drive β-diversity formation by influencing the dispersal and migration of species, the importance of which has not been reported in previous studies. Assessing the impact of co-occurrence patterns on β-diversity is important for understanding the mechanisms of diversity formation. Our study highlights the influence of microbial co-occurrence patterns on β-diversity and combines the drivers of community β-diversity with drought variation, revealing that drought indirectly affects β-diversity by influencing diazotrophic co-occurrence patterns and community assembly.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake

The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.

The Plant Microbiome: From Ecology to Reductionism and Beyond

Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.