Soil Niches Research Articles

Bacterial Diversity in the Different Ecological Niches Related to the Yonghwasil Pond (Republic of Korea).

The bacteriome profile was studied in freshwater ecosystems within the Yonghwasil pond, situated at the National Institute of Ecology, Seocheon-gun, Chungcheongnam-do, central western Korea. Six samples from water, mud, and soil niches were assessed, specifically from lake water, bottom mud (sediment), and root-soil samples of Bulrush, wild rice, Reed, and Korean Willow. Notably, the phylum Actinobacteria exhibited an upward trend moving from water to mud to soil samples, whereas Chloroflexi showed a contrasting decrease. Across the board, Proteobacteria emerged as the reigning phylum, and subsequent dominance was attributed to Firmicutes and Actinobacteria. The water samples were characterized by an enriched presence of Cyanobacteria and Bacteroidetes, whereas the mud samples distinctly housed a higher concentration of Chloroflexi. Assessing biodiversity through OTU and ACE indices revealed a subdued species richness in the water samples. On the contrary, mud samples stood out with the highest OTU and ACE metrics, signifying a microbially diverse habitat. Bulrush, wild rice, Reed, and Willow samples showed intermediate microbial diversity. The Shannon index further corroborated the pronounced microbial diversity in mud and Bulrush habitats with others. This research elucidates the microbial intricacies across different habitats within Yonghwasil Pond, emphasizing the pivotal role of environmental matrices in shaping bacterial communities.

Soil Microbiota Modulates Root Transcriptome With Divergent Effect on Maize Growth Under Low and High Phosphorus Inputs

ABSTRACTPlant growth can be promoted by beneficial microorganisms, or inhibited by detrimental ones. Although the interaction process between a single microbial species and its host has been extensively studied, the growth and transcriptional response of the host to soil microbiota is poorly understood. We planted maize in natural or sterile soil collected from a long‐term experimental site with two different soil phosphate (P) regimes. We examined the composition of microbial communities inhabiting root‐associated niches in natural soil. In parallel, we determined the biomass, ionomes, and root transcriptome profiling of maize grown in natural or sterile soil. Soil microbiota could promote or inhibit different P starvation‐responsive (PSR) genes, as well as induce several defense‐related metabolic processes independently of external P levels. Soil microbiota accompanied by long‐term application of P fertilizer induced lower intensity of PSR and defense responses, inhibiting maize growth. Under a low P regime, the PSR and defense responses were induced to a higher extent, promoting P absorption and growth. Our findings suggest a soil P‐dependent effect of microbiota on maize growth by integrating PSR and defense responses and provide a more refined understanding of the interaction between root growth and soil microbiota.

Spatiotemporal distribution prediction of the relict and endangered plant Tetraena mongolica in inner Mongolia, China under climate change

Climate change significantly affects the distribution of plant species, particularly that of relict plants. Tetraena mongolica Maxim. is a first-class endangered relict plant in China, primarily found in Inner Mongolia. This study explored the impact of multiple factors on its potential distribution under climate change. Considering a comprehensive set of 42 potential influencing variables, including climate, soil, net primary productivity (NPP), human activities, and topography, 29 variables were selected. The maximum entropy (MaxEnt) model was used to construct separate climate and soil niche models, and an “overlay function” was employed to construct a dual-suitability model. By establishing five different scenarios, we analyzed the effects of climate, human activities, and NPP on T. mongolica distribution. The results showed that climate is the most significant factor, soil constraints limit its distribution, and human activities reduce its suitable habitats. Although the direct influence of NPP is limited, it may indirectly affect T. mongolica distribution by improving habitat conditions. Future climate change is expected to sharply reduce suitable habitat areas, with the center of distribution migrating eastward. The study’s findings imply that climate change, human activities, and soil conditions significantly impact the distribution and survival of the endangered plant T. mongolica, necessitating comprehensive conservation measures to mitigate habitat loss and ensure its preservation.

The epidemic occurrence of decline disease in bayberry trees altered plant and soil related microbiome and metabolome

BackgroundIn China, decline disease with unknown etiology appeared as an epidemic among bayberry trees in the southern area of the Yangtze River. Furthermore, the use of beneficial microbes has been reported to be able to reduce the incidence of this disease, emphasizing the association of this disease with microorganisms. Therefore, it has become critical to uncover the microbiome’s function and related metabolites in remodeling the immunity of bayberry trees under biotic or abiotic stresses.ResultsThe amplicon sequencing data revealed that decline disease significantly altered bacterial and fungal communities, and their metabolites in the four distinct niches, especially in the rhizosphere soils and roots. Furthermore, the microbial communities in the four niches correlated with the metabolites of the corresponding niches of bayberry plants, and the fungal and bacterial networks of healthy trees were shown to be more complex than those of diseased trees. In addition, the role of microbiome in the resistance of bayberry trees to the occurrence of decline disease was justified by the isolation, identification, and characterization of important microorganisms such as significantly enriched Bacillus ASV804, Pseudomonas ASV815 in healthy plants, and significantly enriched Stenotrophomonas ASV719 in diseased plants.ConclusionOverall, our study revealed that the occurrence of decline disease altered the microbiome and its metabolites in four ecological niches in particular rhizosphere soils and roots of bayberry, which provides new insight into the control of bayberry decline disease.

The Combination of Buchloe dactyloides Engelm and Biochar Promotes the Remediation of Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in promoting soil improvement, the mechanism of biochar removing soil PAHs through rhizosphere effect in the process of phytoremediation remain uncertain. In this study, the regulation of soil niche and microbial degradation strategies under plants and biochar were explored by analyzing the effects of plants and biochar on microbial community composition, soil metabolism and enzyme activity in the process of PAH degradation. The combination of plants and biochar significantly increased the removal of phenanthrene (6.10%), pyrene (11.50%), benzo[a]pyrene (106.02%) and PAHs (27.10%) when compared with natural attenuation, and significantly increased the removal of benzo[a]pyrene (34.51%) and PAHs (5.96%) when compared with phytoremediation. Compared with phytoremediation, the combination of plants and biochar significantly increased soil nutrient availability, enhanced soil enzyme activity (urease and catalase), improved soil microbial carbon metabolism and amino acid metabolism, thereby benefiting microbial resistance to PAH stress. In addition, the activity of soil enzymes (dehydrogenase, polyphenol oxidase and laccase) and the expression of genes involved in the degradation and microorganisms (streptomyces, curvularia, mortierella and acremonium) were up-regulated through the combined action of plants and biochar. In view of the aforementioned results, the combined application of plants and biochar can enhance the degradation of PAHs and alleviate the stress of PAH on soil microorganisms.

Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus.

Kinases that synthesize inositol phosphates (IPs) and pyrophosphates (PP-IPs) control numerous biological processes in eukaryotic cells. Herein, we extend this cellular signaling repertoire to viruses. We have biochemically and structurally characterized a minimalist inositol phosphate kinase (i.e., TvIPK) encoded by Terrestrivirus, a nucleocytoplasmic large ("giant") DNA virus (NCLDV). We show that TvIPK can synthesize inositol pyrophosphates from a range of scyllo- and myo-IPs, both in vitro and when expressed in yeast cells. We present multiple crystal structures of enzyme/substrate/nucleotide complexes with individual resolutions from 1.95 to 2.6 Å. We find a heart-shaped ligand binding pocket comprising an array of positively charged and flexible side chains, underlying the observed substrate diversity. A crucial arginine residue in a conserved "G-loop" orients the γ-phosphate of ATP to allow substrate pyrophosphorylation. We highlight additional conserved catalytic and architectural features in TvIPK, and support their importance through site-directed mutagenesis. We propose that NCLDV inositol phosphate kinases may have assisted evolution of inositol pyrophosphate signaling, and we discuss the potential biogeochemical significance of TvIPK in soil niches.

Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized (sym) Genes in the Polytypic Species Neorhizobium galegae

Nodule bacteria (rhizobia) represent a suitable model to address a range of fundamental genetic problems, including the impacts of natural selection on the evolution of symbiotic microorganisms. Rhizobia possess multipartite genomes in which symbiotically specialized (sym) genes differ from core genes in their natural histories. Diversification of sym genes is responsible for rhizobia microevolution, which depends on host-induced natural selection. By contrast, diversification of core genes is responsible for rhizobia speciation, which occurs under the impacts of still unknown selective factors. In this paper, we demonstrate that in goat’s rue rhizobia (Neorhizobium galegae) populations collected at North Caucasus, representing two host-specific biovars orientalis and officianalis (N2-fixing symbionts of Galega orientalis and G. officinalis), the evolutionary mechanisms are different for core and sym genes. In both N. galegae biovars, core genes are more polymorphic than sym genes. In bv. orientalis, the evolution of core genes occurs under the impacts of driving selection (dN/dS > 1), while the evolution of sym genes is close to neutral (dN/dS ≈ 1). In bv. officinalis, the evolution of core genes is neutral, while for sym genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and sym genes revealed using ANI analysis may be due to a low intensity of gene transfer within and between N. galegae biovars. Polymorphism in both gene groups and the impacts of driving selection on core gene evolution are more pronounced in bv. orientalis than in bv. officianalis, reflecting the diversities of their respective host plant species. In bv. orientalis, a highly significant (P0 < 0.001) positive correlation is revealed between the p-distance and dN/dS values for core genes, while in bv. officinalis, this correlation is of low significance (0.05 < P0 < 0.10). For sym genes, the correlation between p-distance and dN/dS values is negative in bv. officinalis but is not revealed in bv. orientalis. These data, along with the functional annotation of core genes implemented using Gene Ontology tools, suggest that the evolution of bv. officinalis is based mostly on adaptation for in planta niches while in bv. orientalis, evolution presumably depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented, suggesting that gene nucleotide polymorphism may be extended by driving selection only in ecologically versatile organisms capable of supporting a broad spectrum of gene alleles in their gene pools.

Evaluation of 16S rRNA gene primer pairs for bacterial community profiling in an across soil and ryegrass plant study

AbstractIntroductionAs microbes play important roles in many hosts and niches, linking microbiota across niches is becoming an important area of research. Studying microbiota across multiple niches would allow understanding of ecosystem‐level interactions and potential points of better manipulation for agriculture gains. However, a suitable methodology to characterize microbiota from vast different niches is currently lacking. We used the plant shoot and soil as two important niches for this case study.Materials and MethodsConsidering the important linkage plant play in connecting above‐ and below‐ground ecosystems and challenges of working with plant microbiota, we first compared three commonly used 16S ribosomal RNA gene primer pairs targeting V3–V4 or V5–V7 regions coupled with Illumina sequencing for bacterial communities associated with ryegrass shoot. Then the selected primer was used to amplify bacterial communities in soil and rhizosphere samples for comparison with the commonly used 338F/806R. Finally, core operational taxonomic units (OTUs) across soil and plant niches were identified.ResultsPrimer pair 799F/1193R amplified the lowest number of plant organelle sequences (<0.2% of total sequences) and consistently showed the highest α‐diversity compared with 338F/806R and 335F/769R. For soil and rhizosphere samples, 799F/1193R also demonstrated significantly higher α‐diversity indices compared with 338F/806R. The bacterial phyla commonly detected by both primer pairs comprised >97% of the total relative abundance in soil and rhizosphere samples. In addition, the differences in bacterial communities of the soil and rhizosphere samples were more evident when using 799F/1193R than 338F/806R. Using the 799F/1193R data set, 50 core bacterial OTUs were identified across soil, rhizosphere and shoot niches, whereas only 38 core OTUs were identified when using 338F/806R. Most of these core OTUs were dominant in either shoot or soil niche.ConclusionPrimer pair 799F/1193R is suitable for bacterial community studies targeting ryegrass plant and soil microbiota, in particular for cross‐niches studies.

Legume-cereal intercropping as a strategy of regenerative agriculture supporting reverse of biodiversity loss - relevance of microbiome-based research

Adverse environmental impacts connceted with high chemicals and fertilizers use is one of the causes of biodiversity loss. Therefore, there is a need to looking for more natural and non-hazardous alternative approaches to make agriculture more sustain. The legume-cereal intercropping is currently one of the „hot topics” in the area of sustainable and regenerative agriculture. These intercropping practices are increasingly gaining attention as a way for enhancing soil ecosystem services and reversal biodiversity loss, as well as as a strategy of harnesing plant yield quality and soil health. Legume-cereal systems are the most common intercropping combinations used in sustainable agriculture models because of their noncompeting niche requirements and atmospheric nitrogen fixation which improve a balance of this nutrient in soil and plant and decrease the amount of mineral fertilizers use. However, conventional crop rotations in the EU are largely dominated by cereals while legume cultivation has declined in recent years. The idea of the LEGUMINOSE project includes that multi-species assemblages of plants deliver rhizosphere functions that are greater than the sum of the functions delivered by the rhizospheres of individual plants growing alone as a monoculture. We hypotheses that the higher plant diversity in intercropping will increase plant health, improve soil biodiversity and reduce the use of pesticides in agroecosystems. However ther is a knowledge gap concerning plant-soil-microbe interactions under root exudation from single and diverse plant assemblage and role of soil microbiomes in soil ecosystem functionality and plant production. Therefore we will focus on understanding these interactions by the microbiome research of soil and plant niches, including bulk soil, rhisozphere, roots and shoots of cereal and legume plants in order to assess the percentage of microbiota transfered between them within monocropping and intercropping fields and understand relationships of that microbiomes in plant health improvement. This project will design and implement sustainable environmental practices based on legume-cereal intercropping systems that account for the nature, impacting to global biogeosphere changes. Research funded in the frame of Horizon Europe Programme, agreement no. Project 101082289 — LEGUMINOSE.

'Follow the Water': Microbial Water Acquisition in Desert Soils.

Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.

Plant and soil health in organic strawberry farms – Greater importance of fungal trophic modes and networks than α-diversity of the mycobiome

The mycobiome composition and health status of host plants are closely related. These relationships should be studied and recognized, as they may form the basis of future sustainable agriculture. The aim of this study was to select relevant biological indicators for monitoring soil microbial diversity by revealing characteristic differences between the mycobiomes of various soil compartments (bulk and rhizosphere) and plant niches (roots and shoots) from 13 healthy and diseased organic strawberry farms. The results of this study show that α-diversity of the mycobiome is less important in shaping plant health than fungal trophic mode composition. Healthy soil niches and roots contain less core taxa, but more differentially abundant taxa, than unhealthy ones. The results also suggest that plant health was shaped by more than just the most abundant fungal taxa, indicating that rare taxa should not be neglected in the analysis of mycobiome structure. We also demonstrate that fungal communities in the soil and plant niches from healthy strawberry farms create more stable and steady networks as compared to those from unhealthy farms. Finally, we show that the mycobiome roots-shoot axis is an important trait to consider in unhealthy plants from strawberry farms.

Assessment of the impact of climate change on endangered conifer tree species by considering climate and soil dual suitability and interspecific competition

Climate change results in the habitat loss of many conifer tree species and jeopardizes species biodiversity and forest ecological functions. Delineating suitable habitats for tree species via climate niche model (CNM) is widely used to predict the impact of climate change and develop conservation and management strategies. However, the robustness of CNM is broadly debated as it usually does not consider soil and competition factors. Here we developed a new approach to combine soil variables with CNM and evaluate interspecific competition potential in the niche overlapping areas. We used an endangered conifer species - Chamaecyparis formosensis (red cypress) - as a case study to predict the impact of climate change. We developed a novel approach to integrate the climate niche model and soil niche model predictions and considered interspecific competition to predict the impacts of climate change on tree species. Our results show that the suitable habitat for red cypress would decrease significantly in the future with an additional threat from the competition of an oak tree species. Our approach and results may represent significant implications in making conservation strategies and evaluating the impacts of climate change, and providing the direction of the refinement of the ecological niche model.

Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes.

This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development.

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction.

There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.

Degradation of commercial biodegradable plastics and temporal dynamics of associated bacterial communities in soils: A microcosm study

Biodegradable plastics (BDPs) have been introduced to replace conventional fossil-based non-biodegradable plastics in agricultural production to reduce the accumulation of plastic debris in soils. However, the degradation performance of commercially available BDP products in real soils and the response of soil microbial communities to biodegradation remain unclear. Here, we explored the degradation characteristics of a commercial BDP product (made from starch, polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) in different soils in a microcosm system over a period of 360 days. Temporal dynamics of associated bacterial communities in different soil niches (control soil, plastic surface soil and bulk soil (soil without close contact with plastics)) were profiled. Weight loss reached 42.0±1.2% to 48.0±2.2% in different soils after 360 days. The degradation of BDP followed the same pattern in different soils characterized by two distinct stages. In the first stage (day 0–30), BDPs experienced major weight loss (35.8–41.9%) which coincided with a drastic increase in the soil dissolve organic carbon (1.53–2.25 times the control soil) and the forming of distinct bacterial communities in the plastic surface soil. Thermalgravimetric analysis (TGA) and fourier transform infrared (FTIR) analysis confirmed the fast depletion of starch in this stage. In addition, observations with naked eyes and scanning electron microscope confirmed intensive microbial colonization on BDP surfaces. In the second stage (day 30–360), the degradation of remaining PLA and PBAT continued at a relatively slow rate. Meanwhile bacterial communities in the plastic surface soil started to gradually recover from the disturbance caused by fast biodegradation in the first stage in a soil-dependent manner. Our findings indicate that the degradation performance of BDPs was limited by the degradation rate of relatively recalcitrant components and the temporal dynamics of associated soil bacterial communities synchronized with the degradation of BDPs.

Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils.

Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche.

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.

Community Characteristics and Niche Analysis of Soil Animals in Returning Farmland to Forest Areas on the Loess Plateau

Niche theory is significant for understanding the function of community structure, interspecific relationships, and community dynamic succession. However, there are few studies on the soil animal niche in returning farmland to forest areas on the Loess Plateau, making it challenging to comprehend the utilization of soil animal resources, the stability of the local community, and the succession process in the areas. Therefore, this study collected soil animals in five typical vegetation types: Robinia pseudoacacia (R), Hippophae rhamnoides (H), Populus simonii (P), Pinus tabulaeformis (T), and Armeniaca sibirica x Hippophae rhamnoides (M), with abandoned grassland (G) used as a control group. Then, the number of soil animal taxa, individuals, diversity, and niche were sampled and examined in the study areas during the four seasons of spring, summer, autumn, and winter using the manual sorting method and the Tullgren method. The results revealed that 3872 soil animals from 3 Phyla, 8 Classes, 22 Orders, and 49 Families were captured in the study areas. The dominant groups of soil macrofauna were Diptera larvae, Julidae, and Formicidae, and the dominant groups of meso–micro soil fauna were Oribatida, Protospira, and Collembola juveniles. Soil animals have rich nutritional function groups, with the most saprophytic soil animal groups. The individual density and taxa number of soil animals in G were lower than other vegetation on the whole. H, M, and P had a higher Shannon–Winner index than the other vegetation. Seasonal changes had different effects on macro and meso–micro soil fauna. The diversity of soil macrofauna is higher in spring and summer, and that of meso–micro soil fauna is higher in autumn and winter. Oribatida, Diptera Larvae, and Formicidae had a large niche width in the main taxa of soil animals, with universal adaptability to the environment. Cicadellidae and Culicidae had narrow niche widths and were highly dependent on resources and the environment. There were 67 pairs of highly overlapped (Oik > 0.8) taxa of soil animals and 56 pairs of moderately overlapped (0.6 < Oik ≤ 0.8) taxa, accounting for 80.39% of the total number of taxa. Soil animals had high commonality in resource utilization, intense competition, and poor community stability. As a result, we can conclude that the soil animal community in the study areas was in the stage of succession.

Experimental assessment of forest floor geophyte and hemicryptophyte impact on arbuscular mycorrhizal fungi communities

PurposeHerbaceous plants are important components of temperate forest structure and its functioning, however, their impacts on arbuscular mycorrhizal fungi (AMF) remain largely unexplored. We studied the influence of forest herbaceous plant species on AMF abundance, morphospecies richness, and community composition in soil.MethodsWe tested the influence of plant species identity in an outdoor mesocosm experiment, using two soils, differing in physicochemical properties, planted with four plant species of contrasting traits related to morphology, phenology, reproduction, and ecology; the hemicryptophyte, summer-green Aegopodium podagraria, and spring ephemeral geophytes comprising Allium ursinum, Anemone nemorosa, and Ficaria verna. The plants were grown on both soils in four monocultures, in a combination of A. podagraria and A. ursinum, and a mixture of all four species.ResultsAegopodium podagraria and A. ursinum promoted AMF abundance and diversity the most. Higher AMF root colonization and/or soil concentrations of AMF structural and storage markers 16:1ω5 PLFA and NLFA, as well as higher AMF spore and morphospecies numbers were found in the A. podagraria and A. ursinum monocultures and mixture. The short period of photosynthetic activity of A. ursinum due to rapid leaf decay does not negatively affect the symbiosis with AMF. Although A. nemorosa and F. verna are mycorrhizal, their effect on AMF in soil was weak.ConclusionsThe plant impact on AMF may be related to the differences in plant coverage and the character of their interactions with AMF. The herbaceous plants can form niches in soil differing in AMF abundance and diversity.