Abundant Subcommunities Research Articles

Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake.

The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH4+-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.

Diversity patterns and ecological assembly mechanisms of bacterial communities in the northeastern Indian Ocean epipelagic waters during the northeast monsoon

Disentangling microbial community diversity patterns and assembly mechanisms is critical for understanding ecological processes and evaluating biogeochemical cycling in ecosystems. However, the diversity patterns and assembly mechanism of the microbial communities in the epipelagic waters in the northeastern Indian Ocean (NEIO) on the spatial scale are still unclear. In this study, we investigated the spatial dynamics, geographic distribution pattern, and assembly process of the bacterial community using 532 samples collected from the epipelagic waters in the NEIO during the northeast monsoon. The results indicate that the bacterial richness and Bray-Curtis dissimilarity exhibited the strongest correlations with depth compared to the latitudinal and longitudinal scales. The dissolved oxygen was identified as the most important environmental factor affecting the bacterial richness and Bray-Curtis dissimilarity compared to temperature and salinity. The distance–decay relationship (DDR) of the bacterial community strengthened with increasing water depth. Turnover was the predominant β-diversity component influencing the spatial changes in the whole bacterial community. The dispersal limitation of the stochastic process and homogeneous selection of the deterministic process governed the bacterial ecological assembly process of the whole bacterial community. Abundant and rare subcommunities differed in terms of the niche breath, composition changes. The abundant subcommunities exhibited a much wider niche breath than the rare subcommunities. Regarding the abundant subcommunity species changes, the contributions of the turnover and nestedness varied with the water depth and oceanic region. In contrast, turnover was the major β-diversity component regarding the changes in the rare species. These data improve our understanding of the ecological processes of bacterial community assemblages in the NEIO.

Bacterial rarity in a subarctic stream network: Biodiversity patterns, assembly mechanisms and types of rarity.

Dendritic stream networks are an intriguing subject for exploring the spatial and temporal variability of the rare and common bacterial biosphere, yet very few such studies have been conducted. We sampled riverine bacterioplankton at 13 sites in a subarctic riverine network across 3 years, with five sampling times each year. Ordinations showed a consistent pattern of downstream shift for both rare and abundant subcommunities. We also detected a temporal signal, with seasonal community shifts reflecting changes in water temperature and groundwater contribution, and an inter-annual pattern where the year 2018 differed from other years. Phylogenetic turnover of the rare subcommunity indicated homogeneous selection, whereas the abundant subcommunity was mainly stochastically structured. Transiently rare taxa were the dominant type of rarity with the highest proportion at the headwater regions. The bacterioplankton community was characterized by a small group of core taxa that occurred at most sites with little temporal variation, a very large number of permanently or transiently rare taxa, and taxa shifting through time between the rare and abundant biosphere. While this basic structure could have been detected with less extensive temporal replication, a comprehensive understanding of the rare biosphere in riverine bacterioplankton can only be achieved via inter-annual, spatially replicated sampling that covers the whole stream network.

Ecological succession of abundant and rare subcommunities during aerobic composting in the presence of residual amoxicillin

Aerobic composting increases the content of soluble nutrients and facilitates the safe treatment of livestock manure. Although different taxa play crucial roles in maintaining ecological functionality, the succession patterns of community composition and assembly of rare and abundant subcommunities during aerobic composting under antibiotic stress and their contributions to ecosystem functionality remain unclear. Therefore, this study used 16 S rRNA gene sequencing technology to reveal the response mechanisms of diverse microbial communities and the assembly processes of abundant and rare taxa to amoxicillin during aerobic composting. The results indicated that rare taxa exhibited distinct advantages in terms of diversity, community composition, and ecological niche width compared with abundant taxa, highlighting their significance in maintaining ecological community dynamics. In addition, deterministic (heterogeneous selection) and stochastic processes (dispersal limitation) play roles in the community succession and functional dynamics of abundant and rare subcommunities. The findings of this study may contribute to a better understanding of the relative importance of deterministic and stochastic assembly processes in composting systems, and the ecological functions of diverse microbial communities, ultimately leading to improved ecological environment.

Abundant and Rare Microbial Subcommunities in Soda Lake Nukhe-Nur (Barguzin Depression, Russia)

In this study, we first investigated the composition of microbial communities of abundant, intermediate and rare subcommunities in soda Lake Nukhe-Nur (the Barguzin Basin) using Illumina MiSeq high-throughput sequencing. The results showed that abundant subcommunities mainly consisted of Pseudomonadota, Cyanobacteriota, Bacteroidota и Bacillota. In contrast, the rare subcommunities in the microbial mats were mainly composed of Pseudomonadota, Cyanobacteriota, Bacillota, Deinococcota, Gemmatimonadota, Bacteroidota, Actinobacteriota, Kiritimatiellaeota. In the rare subcommunity of the bottom sediments, Euryarchaeota, Actinobacteriota, Pseudomonadota, Bacillota, Bacteroidota, Chloroflexota, Gemmatimonadota, Verrucomicrobiota, Epsilonbacteraeota, and Deinococcota were found. However, the dominant phyla of the abundant subcommunity were also found in the intermediate and rare subcommunities. The predictive analysis of the microbial ecological function has revealed a broad potential diversity of metabolic pathways in the abundant, intermediate, and rare subcommunities of microbial mats and bottom sediments in Lake Nukhe-Nur. In soda lakes, rare subcommunities may play a greater role in the decomposition of organic matter than do abundant subcommunities. Overall, this study provides a better understanding of the microbial community structure and potential ecological functions of abundant and rare subcommunities in soda lakes ecosystems. The identified rare taxa open new opportunities for ecological, taxonomic, and genomic discoveries in Barguzin soda lakes.

Divergent adaptation strategies of abundant and rare bacteria to salinity stress and metal stress in polluted Jinzhou Bay

Understanding how abundant (AT) and rare (RT) taxa adapt to diverse environmental stresses is vital for assessing ecological processes, yet remains understudied. We collected sediment samples from Liaoning Province, China, representing rivers (upstream of wastewater outlet), estuaries (wastewater outlets), and Jinzhou Bay (downstream of wastewater outlets), to comprehensively evaluate AT and RT adaptation strategies to both natural stressors (salinity stress) and anthropogenic stressors (metal stress). Generally, RT displayed higher α- and β-diversities and taxonomic groups compared to AT. Metal and salinity stresses induced distinct α-diversity responses in AT and RT, while β-diversity remained consistent. Both subcommunities were dominated by Woeseia genus. Metal stress emerged as the primary driver of diversity and compositional discrepancies in AT and RT. Notably, AT responded more sensitively to salinity stress than RT. Stress increased topological parameters in the biotic network of AT subcommunities while decreasing values in RT subcommunities, concurrently loosening interactions of AT with other taxa and strengthening interactions of RT with others in biotic networks. RT generally exhibited greater diversity of metal resistance genes compared to AT. Greater numbers of genes related to salinity tolerance was observed for the RT than for AT. Compared to AT, RT demonstrated higher diversity of metal resistance genes and a greater abundance of genes associated with salinity tolerance. Additionally, deterministic processes governed AT community assembly, reinforced by salinity stress. However, the opposite trend was observed in the RT, where the importance of stochastic process gradually increased with metal stresses. The study is centered on exploring the adaptation strategies of both AT and RT to environmental stress. It underscores the importance of future research incorporating diverse ecosystems and a range of environmental stressors to draw broader and more reliable conclusions. This comprehensive approach is essential for gaining a thorough understanding of the adaptive mechanisms employed by these microorganisms.

Assembly processes and ecological dynamics of root-associated bacterial communities during phytoremediation of vanadium-titanium mine tailings using Millettia pinnata

The vanadium-titanium magnetite (V–Ti) mine tailings are a reservoir of heavy metals, posing a grave peril to the adjacent soil environment. Millettia pinnata has emerged as a proficient pioneer tree species for the purpose of phytoremediation of V–Ti tailings. In the course of phytoremediation, the soil microbiota play an indispensable role within the rhizosphere ecosystem. The aim of this study was to dissect the underlying mechanisms governing the assembly processes of the bacterial community. The βNTI and RCbray analyses revealed that while the overall community assembly manifested deterministic attributes, rare taxa were chiefly impacted by stochastic processes (73.7%), inclusive of dispersal limitation and undominated mechanisms. In contrast, the abundant subcommunity was primarily subject to deterministic forces (84.3%), notably heterogeneous selection. Mantel test, regression analysis and ecological niche analysis showed that soil nitrogen availability emerged as a pivotal driver of the microbial assembly processes, exerting substantial influence on both rare (Mantel's r = 0.6817, p = 0.0001) and abundant taxa (Mantel's r = 0.5103, p = 0.0001) by amplifying their diversity and community turnover, constricting habitat niche breadth and overlap, and fostering the proliferation of ecological specialists. However, the heavy metal content was not found to wield significant influence in shaping the structure and assembly of the rhizosphere community (p > 0.05). The present results affirm the proposition that rare taxa are important in upholding ecological stability and providing essential microbial ecosystem services, while abundant taxa serve to fortify the entirety of the community. These insights advance our understanding of the community dynamics pertaining to the rhizosphere community associated with M. pinnata, holding paramount theoretical implications for the endeavour of plant-assisted ecological restoration in polluted tailings sites.

Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China

The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.

Distinct variabilities of soil abundant and rare bacteria relate differently to carbon cycling functionality in eroded ecosystems

Elucidating the interaction between microorganisms and soil carbon cycling functionality (SCCF) in the eroded ecosystems, can improve our understanding of the mechanisms by which soil erosion and deposition affect soil organic carbon pool. Abundant and rare sub-communities are the integral components in driving SCCF. However, changes in abundant and rare sub-communities, as well as their contributions to SCCF, remain unclear in the eroded ecosystems. In this study, changes in abundant and rare sub-communities and their correlations with SCCF were comparatively explored with respect to soil erosion and deposition in the Loess Plateau. The α-diversity of rare sub-communities in the depositional zones was 4% higher than that in the eroding slopes, but there was no significant difference in α-diversity of abundant sub-communities between the eroding slopes and depositional zones. The compositions of abundant and rare sub-communities differed between the eroding slopes and depositional zones. Regarding the co-occurrence network of the eroded ecosystems, abundant sub-communities compared with rare sub-communities presented a higher degree and betweenness centrality; however, rare sub-communities possessed more frequent interactions with other species than abundant sub-communities, especially positive interactions. The α-diversity of abundant and rare sub-communities in ecological clusters showed positive links with SCCF. The link between α-diversity of abundant sub-communities and SCCF was weaker than that with rare sub-communities, which was related to the significant disparity in the abundance of functional genes involved in SCCF and the extent of functional redundancy between abundant and rare sub-communities in the eroded ecosystems. The functional difference of abundant and rare sub-communities in improving SCCF under soil erosion and deposition, is important for accurately assessing the effects of microbial communities on soil organic carbon pool in regions predominated with fragmented eroded landscapes.

Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession

Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.

Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities.

The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.

The assembly, biogeography and co-occurrence of abundant and rare microbial communities in a karst river

Karst rivers are highly susceptible to environmental disturbance due to their robust hydraulic connectivity. However, current knowledge of the mechanisms that regulate the assembly of bacterial and protistan subcommunities in river ecosystems, particularly in karst regions, is limited. By employing 16S and 18S rRNA gene amplicon sequencing, we explored how the diversities and assembly of abundant and rare bacterial and protistan subcommunities adapt to the local environmental variables in a karst river. Both bacterial and protistan rare subcommunities in karst river environments showed a similar biogeography to their abundant subcommunities. Also, a significant distance-decay pattern was observed in all components of the bacterial and protistan subcommunities along the Chishui River, with the rare subcommunities showing a more pronounced distance-decay pattern compared to the abundant subcommunities. Except protist rare subcommunity, the abundant and rare bacterial and abundant protistan subcommunities were strongly structured by the dispersal limitation processes rather than heterogeneous selection. Either bacteria or temperature, elevation and conductivity were the primary drivers for both abundant and rare subcommunities. Additionally, our results suggested that the rare subcommunities contribute significantly to the persistence and stability of microbial networks in the Chishui River, as they exhibited a higher number of keystones compared to the abundant subcommunities. Overall, our study revealed that in the karst river ecosystem, abundant bacterial subcommunities had a higher potential for environmental adaptation than rare bacterial and protistan subcommunities and identified the factors that moderate their assembly processes.

Abundant rather than rare fungi perform a vital role in maintaining the growth of continuous cropped cut chrysanthemum

Soil fungi play key roles in agricultural ecosystem. Yet, little is currently known about the dynamic pattern and driving factors of the rare and abundant fungal subcommunities in response to the short- and long-term continuous cropping. Here, we comparatively investigated the diversity and structure of rare and abundant fungal subcommunities with varying histories of continuous chrysanthemum (Chrysanthemum morifolium Ramat.) cropping, that is, cropping for 1 year (CP1), 6 years (CP6) and 12 years (CP12). The alpha diversity (estimated as Shannon index) of abundant and especially rare fungal subcommunities increased with continuous cropping years. The structure of both rare and abundant subcommunities varied notably with the increasing of continuous cropping years, but the value of dissimilarity for rare taxa (average of 0.988) was significantly higher than for abundant taxa (average of 0.243). The abundant taxon Mortierellomycota and rare taxa Nitrospirae and Elusimicrobia were significantly enriched in the CP12 treatment. Soil rare fungal taxa were mainly affected by the available nutrients (i.e., carbon, nitrogen and phosphorus) and pH, while the abundant fungal taxa were majorly influenced by soil total nutrients. The growth indicators (e.g., plant biomass, plant height, and flower diameter) of cut chrysanthemum significantly decreased under 12-year continuous cropping system. Random forest models showed that abundant rather than rare fungi played key roles in the chrysanthemum growth even though the rare fungi were more significantly affected during continuous cropping.

Rare microbial communities drive ecosystem multifunctionality in acidic soils of southern China

Soil microbial communities are important for maintaining ecosystem multifunctionality, and abundant and rare sub-communities often have fundamentally different characteristics and ecological roles. However, little is known about the links between microbial sub-communities and soil multifunctionality in acidic soils across large spatial scales. Here, we collected 52 soil samples from four locations spanning 961.3 km in the acidic soil region of southern China and characterized bacterial and fungal sub-communities and their contributions to soil multifunctionality. Sub-community compositions of both rare bacteria and rare fungi significantly explained changes in soil multifunctionality, but abundant sub-communities were not significantly related to soil multifunctionality. This suggested that soil multifunctionality might be mainly controlled by rare microbes in acidic soils. Rare fungal α-diversity, rather than rare bacterial α-diversity, was significantly and positively correlated with multifunctionality. Deterministic processes were the primary drivers of the sub-community assembly of rare bacteria and rare fungi and thus might have an important effect on soil multifunctionality. Soil pH was the most dominant soil factor driving rare bacterial and fungal sub-community structures and affecting soil multifunctionality. In the co-occurrence networks of bacterial and fungal communities, most of the keystone taxa were rare species. The numbers of positive interactions of rare fungal taxa, but not rare bacterial taxa, were positively related to soil multifunctionality. Our results provided evidence that rare microbial sub-communities are important for maintaining ecosystem multifunctionality in acidic soils, and rare bacteria and fungi may display the potentially different mechanisms to drive ecosystem functions.

Plant invasion mediates the regulation of topsoil organic carbon sequestration by the fungal community in coastal wetlands

Spartina alterniflora, which is native to the Atlantic coast, has extensively invaded mangroves/marshes and hence seriously altered coastal soil organic carbon (SOC) sequestration along the Pacific coast. Fungi are directly engaged in the SOC cycle, but how the fungal community impacts coastal carbon sequestration in response to S. alterniflora invasion remains unclear. We explored the fungal community shifts in relation to SOC changes by comparing 6 pairs of independent sites (i.e., dominant native plants vs. S. alterniflora) along a 2,500 km coastal transect in southeastern China. Our results showed that the invasion reduced the fungal diversity and shifted the assemblage processes of the abundant subcommunity, not the rare subcommunity, from determinism (0.409) to stochasticity (0.556). The invasion decreased network topological properties (e.g., network size, centrality, natural connectivity, etc.), cohesion, robustness, and the relative abundance of keystone taxa but increased the vulnerability of the fungal community. Importantly, the Shannon index, total cohesion and keystone taxa of the fungal community were significantly positively correlated with SOC concentration, SOC storage and recalcitrant organic carbon (ROC) but not with labile organic carbon (LOC). The structural equation model further showed that the fungal community diversity, complexity and keystone taxa directly regulated SOC storage under S. alterniflora invasion. Overall, we provide new insights into fungal community shifts and cooccurrence patterns under S. alterniflora invasion, helping us better understand the impact of invasion on SOC cycling and its microbial mechanisms, which will benefit future restoration and optimal coastal management.

Distinct ecological mechanisms drive the spatial scaling of abundant and rare microbial taxa in a coastal sediment

AbstractAimRevealing the ecological mechanisms driving the diversity patterns of microbial communities across space and through time is an essential issue in microbial biogeography. This study links microbial spatial scaling with ecological mechanisms, aiming to provide novel mechanistic insights into the biogeographic patterns followed by different types of microbes.LocationBeibu Gulf, a semi‐enclosed oceanic bay located on the southern coast of China.TaxonBacteria, which were further classified as abundant and rare taxa.MethodsBy employing high throughput sequencing, two typical spatial scaling models, diversity‐area (DAR) and distance‐decay relationships (DDR), were investigated for the abundant and rare microbial communities in a coastal sediment ecosystem. Both alpha‐ and beta‐diversity indices were extended to Hill numbers to verify the contribution of abundant and rare taxa to DAR and DDR. The iCAMP approach was used to quantify the contribution of different ecological processes in structuring microbial communities.ResultsStrong spatial scaling patterns were observed for the whole communities and the rare subcommunities but only weak patterns for the abundant subcommunities. Rare subcommunities were mainly responsible for the observed spatial scaling patterns, as confirmed by extending spatial scaling diversity metrics to Hill numbers. Both environmental heterogeneity and local community assembly mechanisms drove the spatial scaling of microbial communities. Strong ecological drift and dispersal limitation underlay the spatial scaling of rare subcommunities, whereas high homogeneous selection weakened the spatial scaling of abundant subcommunities.Main ConclusionsRare taxa were mainly responsible for the biogeographic patterns followed by sediment microbial communities in the Beibu Gulf. Distinct ecological mechanisms underlay the different biogeographic patterns followed by abundant and rare subcommunities.

Core root-associated prokaryotic community and its relationship to host traits across wheat varieties.

The root-associated microbiomes play important roles in plant growth. However, it is largely unknown how wheat variety evolutionary relatedness shapes each subcommunity in the root microbiome and, in turn, how these microbes affect wheat yield and quality. Here we studied the prokaryotic communities associated with the rhizosphere and root endosphere in 95 wheat varieties at regreening and heading stages. The results indicated that the less diverse but abundant core prokaryotic taxa occurred among all varieties. Among these core taxa, we identified 49 and 108 heritable amplicon sequence variants, whose variations in relative abundances across the root endosphere and rhizosphere samples were significantly affected by wheat variety. The significant correlations between phylogenetic distance of wheat varieties and prokaryotic community dissimilarity were only observed in non-core and abundant subcommunities in the endosphere samples. Again, wheat yield was only significantly associated with root endosphere microbiota at the heading stage. Additionally, wheat yield could be predicted using the total abundance of 94 prokaryotic taxa as an indicator. Our results demonstrated that the prokaryotic communities in the root endosphere had higher correlations with wheat yield and quality than those in the rhizosphere; thus, managing root endosphere microbiota, especially core taxa, through agronomic practices and crop breeding, is important for promoting wheat yield and quality.

Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization

Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R2 = 0.15, P < 0.001) and rare (R2 = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R2bacteria = 0.03, P < 0.05; R2fungi = 0.05, P < 0.05) and nitrogen (R2bacteria = 0.03, P < 0.05; R2fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.

Distinct responses of abundant and rare foraminifera to environmental variables in the Antarctic region revealed by DNA metabarcoding

The Antarctic region plays a key role in regulating the Earth’s climate and contains a unique record of environmental change. Foraminifera, a group of shell-bearing protists, are widely used as paleoenvironmental proxies. However, core-based reconstructions of Antarctic paleoenvironments are often hindered by the lack of foraminiferal fossil record. Foraminiferal ancient DNA provides new avenues for understanding environmental change, but the correlation between molecular ecological features of foraminifera and environmental conditions remains poorly understood. Here, we obtained surface sediment samples from the Southern Ocean at water depths ranging from 50 to 4399 m and measured eight environmental variables. We generated a DNA metabarcoding dataset of foraminifera and presented the first assessment of relationships between foraminiferal molecular diversity and environmental variables in the Antarctic region. The results showed that the alpha diversity of whole community and abundant subcommunity was positively correlated with water depth and negatively correlated with temperature, chlorophyll a and pheophytin a, while the alpha diversity of rare subcommunity had no linear correlation with the above environmental variables. Both rare and abundant foraminiferal subcommunities exhibited distance-decay relationships, but only the beta diversity of rare subcommunity showed a significant positive correlation with water depth. This study reveals contrasting biogeographical patterns of abundant and rare foraminifera and their different correlations with Antarctic environmental variables, holding promise to provide more proxies for reconstructing past environments using foraminiferal ancient DNA and more information for predicting the impact of future environmental changes on polar biodiversity.

Distinct mediating patterns between metal filtering and species coexistence of rare and abundant subcommunities in heavily polluted river sediments

It is unknown how anthropogenic pollutants released into freshwater ecosystems affect the assembly processes of microbial communities in river sediment. We used high-throughput sequencing to examine the assembly of rare and abundant subcommunities in a heavily polluted urban river: the Beiyun River in Beijing, China. Although deterministic processes overrode stochastic processes in shaping local rare and abundant subcommunities, there were distinctly different assembly mechanisms of rare and abundant subcommunities. Rare subcommunity assembly was governed more by interspecificinteractions, and environmental selection and dispersal limitation explained only a small fraction of the variation. However, both factors seemed to govern the assembly of abundant subcommunities. Our results implied that microbial co-occurrence associations tended to be higher when rare subcommunities were less driven by community assembly, and that these associations tended to be lower when abundant subcommunities were more driven by community assembly. A balance between the community assembly and species coexistence was exhibited atthesubcommunitylevel. Importantly, we tried to disentangle the assembly process of abundant subcommunities into introduction and colonization processes characterized by the presence/absence and relative abundance datasets. Interestingly, metals explained the highest percentage of spatial variation in the species introduction process. By affecting nutrient availability, metals also shaped the abundant subcommunity in the species colonization process, but this did not surpass nutrient availability. Therefore, disentangling the introduction and colonization processes enhances our understanding of the assembly mechanisms of microbial communities in heavily polluted running water ecosystems at fine geographical scales.