Divergent community assembly processes and multifunctionality contributions of abundant and rare soil bacteria during a 53-year restoration in the Tengger Desert, China

Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community. KEY POINTS: • Seasonal dynamics of soil bacterial communities were studied in Mount Gongga. • The bacterial community was mainly affected by elevation rather than season. • Deterministic processes dominated bacterial community assembly. • The bacterial network was more complex but less stable at EBF than at DCF.

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.

Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall-grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R 2 = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p < 0.050) increased microbial network complexity and robustness, especially during the colder seasons, despite large variations in network size and complexity in different seasons. In addition, the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer. Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem. Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on theterrestrial carbon cycle.

Microorganisms play essential roles in soil-ecosystem multifunctionality. However, the contribution of their community assembly processes, composition, diversity, and keystone species to ecosystem multifunctionality is unclear, especially in tea-plantation ecosystems. In order to assess the effects of various intercropping patterns (tea-plant monoculture and tea plants, respectively, intercropped with soybean, soybean—milk vetch, soybean—red clover, and soybean—smooth vetch) on soil rare and abundant taxa, a field experiment was carried out. We found that tea plantation intercropping with legumes improved the soil-ecosystem multifunctionality by altering the soil environment, and ultimately benefited nutrient absorption and quality improvement of tea leaves. Whether it was in bacteria or fungi, rare taxa had a higher proportion of deterministic processes in community assembly than abundant taxa. Additionally, intercropping practices changed the soil environment, and rare bacterial taxa were assembled and shifted from variable selection to homogeneous dispersal. Intercropping practices significantly changed the bacterial and fungal communities’ composition, and rare taxa had higher α-diversity than abundant taxa. Increasing legume species in intercropping practice enhanced community dissimilarity to the tea monoculture by affecting soil pH, ammonium nitrogen, and nitrate nitrogen. Rare bacterial and fungal β-diversity exhibited stronger positive relationships with ecosystem multifunctionality (both average and multi-threshold approaches) compared to the corresponding abundant taxa. Furthermore, ecosystem multifunctionality under different intercropping practices was closely related to the keystone rare operational taxonomic units, especially rare bacterial species of Chloroflexi. Our results emphasize the disparate feedbacks of rare and abundant taxa to diverse intercropping practices, as well as the important connection between rare bacterial taxa and ecosystem multifunctionality.

The process of urbanization is one of the most important human-driven activities that reshape the natural distribution of soil microorganisms. However, it is still unclear about the effects of urbanization on the different taxonomic soil bacterial community dynamics. In this study, we collected soil samples from highly urbanized the regions of Yangtze River Delta, Beijing-Tianjin-Hebei in China, to explore the bio-geographic patterns, assembly processes, and symbiotic patterns of abundant, moderate, and rare bacterial communities. We found that the number of moderate and rare taxa species were lower than that of abundant taxa, but their α-diversity index was higher than abundant taxa. Proteobacteria, Acidobacteria, Actinobacteria, Bacterioidetes, and Chloroflexi were the dominant phylum across all three sub-communities. And the β-diversity value of rare taxa was significantly higher than those of moderate and abundant taxa. Abundant, moderate, and rare sub-communities showed a weak distance-decay relationship, and the moderate taxa had the highest turnover rate of microbial geography in the context of urbanization. Diffusion limitation was the dominant process of soil bacterial community assembly. The co-occurrence networks of abundant, moderate, and rare taxa were dominated by positive correlations. The network of moderate taxa had the highest modularity, followed by abundant taxa. The main functions of the abundant, moderate, and rare taxa were related to Chemoheterotrophy and N transformations. Redundancy analysis showed that the dispersal limitation, climate, and soil properties were the main factors dominating bio-geographic differences in soil bacterial community diversity. We conclude that human-dominated urbanization processes have generated more uncertain survival pressures on soil bacteria, which resulted in a stronger linkage but weak bio-geographic variation for soil bacteria. In the future urban planning process, we suggest that such maintenance of native vegetation and soil types should be considered to maintain the long-term stability of local microbial ecosystem functions.

Response of abundant and rare microbial taxa to three iron-carbon composite amendments in metal-contaminated agricultural soil.

Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils

Vegetation restoration is critical for improving soil quality and microbial community dynamics in degraded mining areas. This study explored the effects of different vegetation types (grassland, shrubland, and mixed grass–shrub areas) on soil physicochemical properties, organic carbon fractions, and abundant versus scarce microbial taxa assemblies in a Loess Plateau coal mining area. Soil samples from four depths (0–100 cm) were analyzed using high-throughput sequencing for nutrient content; carbon components, soil organic carbon (SOC), particulate organic carbon (POC), mineral-associated organic carbon (MAOC), dissolved organic carbon (DOC), microbial biomass organic carbon (MBC), and readily oxidizable organic carbon (ROC); microbial diversity. Shrubland soils exhibited significantly higher total nitrogen (TN), total phosphorus (TP), and organic carbon components (SOC, MAOC, and POC) than other vegetation types (p &lt; 0.05), with the greatest carbon accumulation noted in the surface layer depths (0–20 cm). Microbial communities displayed vegetation-specific patterns: abundant taxa (e.g., Actinobacteria, Proteobacteria) dominated nutrient cycling and exhibited resilience to environmental gradients, while rare taxa (e.g., Methylomirabilota, Olpidiomycota) correlated strongly with labile carbon fractions (DOC and POC) and demonstrated metabolic flexibility. Mantel tests identified soil pH, TN, and organic carbon components as key drivers of microbial community divergence (p &lt; 0.01). Shrubland vegetation enhanced soil nutrient retention and carbon stabilization, whereas the mixed grass–shrub systems promoted niche partitioning among rare taxa. These findings highlight the roles of vegetation-mediated carbon inputs and environmental filtering in shaping microbial assembly, providing a scientific framework for optimizing restoration strategies in mining ecosystems.

Seasonal dynamics of microbial communities in rhizosphere and bulk soils of two temperate forests

Soil microbial communities are subjected to significant changes over time. The most rapid changes caused by temperature and soil moisture alternations or the by the inflow of fresh organic matter occur during the several hours or days. They are mostly related to the soil microbial activity. Seasonal dynamics are caused by annual variations in temperature and precipitation that affect the microbial community directly or indirectly through the regulation of plant life. The microbial biomass and the taxonomic composition of soil microbial communities vary significantly throughout the year, which should be taken into account when sampling for a comparative analysis of different soils. The long-term dynamics of microbial communities during primary or secondary successions lead to an increase in the total microbial biomass and the fungi/bacteria ratio, as well as to changes in the taxonomic composition of microbial communities. The main factors of the long-term dynamics are the accumulation of soil organic matter, plant successions, and changes in pH. The diversity of microbial communities during long-term dynamics can vary in different ways and does not follow a single trend. The longest dynamics of soil microbial communities are associated with changes in bioclimatic conditions. Information about soil microbial communities of the past can be obtained by studying buried and permafrost soils. The study of future changes in soil microbial communities is possible in experiments with artificial changes in climatic parameters. Plants are a significant factor in the dynamics of soil microbial communities on all timescales; in short-term periods, the major role is played by the activity of plants; in the long-term trends, the changes in the vegetation abundance and diversity are the most important factors.

The growth and adaptability of desert plants depend on their rhizosphere microbes, which consist of a few abundant taxa and numerically dominant rare taxa. However, the differences in diversity, community structure, and functions of abundant and rare taxa in the rhizosphere microbiome of the same plant in different environments remain unclear. This study focuses on the rhizosphere microbial communities of Artemisia desertorum, a quintessential desert sand-stabilizing plant, investigating the diversity patterns and assembly processes of rare and abundant taxa across four Chinese deserts: Mu Us, Kubuqi, Tengger, and Ulan Buh. The results show that climatic factors, especially aridity and mean annual precipitation (MAP), significantly influence bacterial community composition and microbial network complexity. The interactions between rare and non-rare taxa are non-random, forming a modular network in which rare taxa serve as central nodes, and their loss could destabilize the network. Rare taxa are primarily shaped by heterogeneous selection, whereas abundant taxa are mainly influenced by dispersal limitation. Functionally, abundant taxa exhibit higher metabolic potential, whereas rare taxa are more involved in processes such as cell motility, indicating distinct ecological roles. These results provide new insights into the ecological functions of rare and abundant taxa in desert rhizosphere communities and highlight the importance of microbial management for desert plant health.

Biogeographic pattern of bacterioplanktonic community and potential function in the Yangtze River: Roles of abundant and rare taxa

Co-occurrence patterns and assembly processes of abundant and rare bacterioplankton in plain river network areas of eastern China

There are differences in the environmental adaptability and regulation of nutrient cycling between abundant and rare bacterial communities during the development of planted forest ecosystems. In this study, we aimed to elucidate the relationships between the soil characteristics and the composition and diversity of abundant and rare bacteria across a chronosequence (i.e., 13-yr, 25-yr, 38-yr, 58-yr-old stands) of Pinus massoniana. Abundant bacterial OTUs, richness, and Shannon index showed a different variation with stand age compared with the rare taxa bacterial community. Both abundant and rare bacterial communities showed significant differences between the 13-yr and 25-yr-old stands, but were similar in the 38-yr and 58-yr-old stands. The dominant phyla were Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria, and Planctomycetes in both abundant and rare taxa. However, the same phylum of abundant and rare taxa was inconsistent across the four forest ages. Network analysis further demonstrated that rare taxa had a greater network scale and complexity than abundant taxa, which may contribute to buffering the environmental stress. The Mantel test showed that soil pH, nitrogen pool (i.e., MBN, NH4+, NAlkali), and enzyme activities were the key factors that were associated with the changes in abundant bacterial diversity and structure during the development of P. massoniana. However, more soil variables (i.e., pH, SW, MBN, NH4+, NAlkali, AP, nitrite reductase, and sucrase) regulated the rare bacterial communities. Our results indicate that rare taxa are important contributors to soil bacterial community diversity, and their community dynamics responded to changes in soil physicochemical properties significantly distinct from the abundant taxa. We suggest that future studies should focus more on the response of different taxa subcommunities, rather than on the community as a whole, when studying the changes in microbial community dynamics.