Continuous planting of Chinese fir monocultures significantly influences dissolved organic matter content and microbial assembly processes

Monoculture plantations in China, characterized by the continuous cultivation of a single species, pose challenges to timber accumulation and understory biodiversity, raising concerns about sustainability. This study investigated the impact of continuous monoculture plantings of Chinese fir (Cunninghamia lanceolata [Lamb.] Hook.) on soil properties, dissolved organic matter (DOM), and microorganisms over multiple generations. Soil samples from first to fourth-generation plantations were analyzed for basic chemical properties, DOM composition using Fourier transform ion cyclotron resonance mass spectrometry, and microorganisms via high-throughput sequencing. Results revealed a significant decline in nitrate nitrogen content with successive rotations, accompanied by an increase in easily degradable compounds like carbohydrates, aliphatic/proteins, tannins, Carbon, Hydrogen, Oxygen and Nitrogen- (CHON) and Carbon, Hydrogen, Oxygen and Sulfur- (CHOS) containing compounds. However, the recalcitrant compounds, such as lignin and carboxyl-rich alicyclic molecules (CRAMs), condensed aromatics and Carbon, Hydrogen and Oxygen- (CHO) containing compounds decreased. Microorganism diversity, abundance, and structure decreased with successive plantations, affecting the ecological niche breadth of fungal communities. Bacterial communities were strongly influenced by DOM composition, particularly lignin/CRAMs and tannins. Continuous monoculture led to reduced soil nitrate, lignin/CRAMs, and compromised soil quality, altering chemical properties and DOM composition, influencing microbial community assembly. This shift increased easily degraded DOM, accelerating soil carbon and nitrogen cycling, ultimately reducing soil carbon sequestration. From environmental point of view, the study emphasizes the importance of sustainable soil management practices in continuous monoculture systems. Particularly the findings offer valuable insights for addressing challenges associated with monoculture plantations and promoting long-term ecological sustainability.

Ecological succession and community assembly of mixed microbial culture polyhydroxyalkanoate production systems: Drivers of polyhydroxyalkanoate synthesis and Bdellovibrio predation

The production of polyhydroxyalkanoate (PHA) by mixed microbial culture (MMC) can reduce the pollution of plastics. Ecophysiological study of the microbial community assembly and succession is helpful for comprehensive understanding the MMC PHA production process. The operation mode of sequential aerobic dynamic discharge - aerobic dynamic feeding (ADD-ADF) was applied and the operation can be divided into acclimation phase and maturation phase. Deterministic process caused by selective pressure dominated the community assembly throughout the operation. In the acclimation phase, the physical selective pressure recovered the settling capacity of the system, and settling ability of the MMC was closely related to function of PHA synthesis. However, in the maturation phase, stochastic process caused sludge bulking, making the settling ability and PHA synthesis function of the MMC independent on each other. Stochastic process led to the succession of the dominant PHA-producing bacteria, for example, the predation of Paracoccus and Thauera by Bdellovibrio.

A comprehensive insight into the abundance and community of anammox bacteria in sediments of Hangzhou Bay, China

A total of 13 surface sediments were collected from Hangzhou Bay (HZB) for an investigation into the distribution and influencing factors of anammox bacterial community. The anammox bacterial 16S rRNA and hzo genes ranged between 2.34 × 105 to 9.22 × 105 copies/g and 3.68 × 105 to 1.70 × 106 copies/g, respectively. The results of high throughput sequencing (HTS) revealed that the obtained OTUs were affiliated with five known genera, named Ca. Scalindua, Ca. Jettenia, Ca. Brocadia, Ca. Kuenenia and Ca. Anammoxoglobus. RDA analysis indicated that salinity, pH, and water depth influenced the anammox bacterial community. Furthermore, network analysis identified Ca. Scalindua as a key genus. Neutral community model (NCM) and modified stochasticity ratio (MST) indicated that the deterministic process dominated the anammox bacterial community assembly. Overall, this study offers a more comprehensive understanding of the abundance and community of anammox bacteria in the sediments of HZB.

Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water

Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.

Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67-14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.

Nitrogen addition promotes soil microbial beta diversity and the stochastic assembly

Nitrogen (N) deposition is one of major environmental concerns and alters the microbial communities in the pedosphere. A central debate in governing microbial community is on the relative importance of deterministic (ecological selection) vs. stochastic processes (dispersal, drift, diversification or speciation), which consequently limited our understanding of microbial assembly in response to N addition. Here, we conducted a global analysis of high-throughput sequencing data to reveal the mechanisms of N-addition effects on soil microbial communities. The results show that N addition significantly shifted the microbial community structure and promoted microbial beta diversity, particularly in the N-limited ecosystems. Changes in microbial structure and beta diversity increased significantly as the N addition rate, study duration, and the degree of soil acidification increased. The stochastic processes are more important than the deterministic processes for microbial community assembly, while N addition significantly increase the importance of stochastic processes whether the phylogenetic relationship is considered or not. Overall, the current study highlights the important of ecological stochasticity in regulating microbial assembly under N deposition scenarios.

N-induced root exudates mediate the rhizosphere fungal assembly and affect species coexistence

Root exudates play essential roles in shaping root-associated microbial communities in plant-soil systems. However, knowledge regarding the influence of root exudates on soil communities, particularly concerning their assembly processes and species coexistence patterns, remains limited. In this study, we performed a 20-month pot experiment using a nitrogen (N) addition gradient (0, 2.5, 5, 7.5, 10, and 15 g N m^-2 yr^-1), amplicon sequencing, and metabolomics to investigate the effect of short-term N addition on the assembly process and species coexistence of fungal communities, as well as their association with root exudates in the rhizosphere and bulk soils around Bothriochloa ischaemum. The results demonstrated that short-term N addition led to distinct differences in the diversity, composition, assembly process, and co-occurrence networks of fungal communities in the rhizosphere and bulk soils. The diversity of fungal communities in the rhizosphere soil increased with the rate of N input and peaked at N10 treatment; this could be correlated with the increased abundance in long-chain organic acids (LCOAs). However, above the threshold N rate of 10 g N m^-2 yr^-1, diversity decreased probably because of the high N-induced inhibitory effect on root exudates (i.e., LCOAs). N addition increased the relative abundance of Sordariomycetes in the rhizosphere and decreased the relative abundance of Mortierellomycetes in the bulk soil, while enhancing the abundance of pathotrophs in both bulk and rhizosphere soils. The rhizosphere fungal community was dominated by a stochastic process at a low N input (N0 and N2.5) and by deterministic processes at a high N input (N10 and N15), which is opposite to the trends in the bulk soil. These fungal assembly processes determine the coexistence of fungal species; deterministic processes lead to less interconnected networks in rhizosphere soils that harbor a more complex network than the bulk soil. Associations between the assembly process and species coexistence in the rhizosphere of B. ischaemum were closely related to the changes in root exudates, such as amino acids, short-chain organic acids, and phenols, which were stimulated by N addition. Collectively, our study emphasizes the key roles of root exudates in the establishment of fungal communities in the plant-soil system and furthers our understanding of plant-microbe interactions.

Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes

Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.

Trophic level drives the host microbiome of soil invertebrates at a continental scale

BACKGROUND

Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.

RESULTS

Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.

CONCLUSIONS

Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates. Video abstract.

Cross-taxon congruence of aquatic microbial communities across geological ages in Iceland: Stochastic and deterministic processes

Biotic groups usually have nonrandom cross-taxon relationships in their biodiversity or compositions across sites, but it is poorly known how such congruence varies across long-term ecosystem development, and what are the ecological processes underlying biodiversity patterns. Here, we examined the cross-taxon congruence in diversity and compositions of bacteria, fungi and diatoms in streams from four regions with different geological ages in Iceland, and further studied their community assembly processes. Bacteria and fungi showed contrasting trends in alpha and gamma diversities across geological ages, while their beta diversity patterns were consistent, being the lowest in the oldest region. The three taxonomic groups had the strongest cross-taxon congruence of beta diversity in the oldest region, while the weakest for intermediate-aged regions. Although environmental variables played important roles in shaping their congruence, biotic interaction had nonnegligible influences. Deterministic processes, being dominant for bacteria and fungi, had the highest relative influence in intermediate-aged regions, whereas diatoms showed higher stochasticity. We proposed a four-phase conceptual model to show how the balance of deterministic and stochastic processes changes across geological ages. Taken together, our results provide an advanced understanding of cross-taxon congruence and community assembly processes for aquatic communities over long-term periods of geological age.

Distinct assembly processes shape bacterial communities along unsaturated, groundwater fluctuated, and saturated zones

The subsurface soil environment through the unsaturated (vadose) zone and saturated (below groundwater table) zone is one of the most active layers in the Earth's surface with biogeochemical interactions. Geochemical variables and geographic distance are key driving forces shaping the distribution of soil microbial communities, but our understandings are mainly limited to surface soil or shallow unsaturated zone (1-3 m beneath the ground). In this study, soil and sediment samples were collected from the unsaturated zone, through groundwater fluctuated zone, to saturated zone (up to 20 m) to unravel the assembly processes mediating vertical bacterial community succession across these three zones. Our results suggested both geochemical niches and bacterial diversity had different vertical patterns in each zone. With increased depth, pH increased and nutrient levels (C, N, P, K) and bacterial diversity declined in the unsaturated zone, and nutrients and bacterial diversity remained low levels after reaching the fluctuated and saturated zones. Nutrients were the key drivers shaping bacterial variation in the unsaturated zone, but limited nutrients and only 'depth' significantly explained the variations in the fluctuated zone and saturated zone, respectively. The co-occurrence network supported a more species co-existence pattern in the unsaturated zone than that in the other two zones. Due to the geochemical variations across three zones, the assembly of phylogenetically more clustered communities was observed through deterministic processes (e.g., 55% homogenizing selection) in the unsaturated zone, but the stochastic process (e.g., 50%-70% dispersal limitation) was more important in the fluctuated and saturated zones. These findings together suggested that the vertical distribution of soil bacterial community assembly was zone-specific and shaped by the degree of deterministic vs. stochastic processes. Our results provide a novel insight into the microbial community assembly across three different ecosystems in the Earth's critical zone and shed a light on subsurface biogeochemical processes.

Monitoring, assessment, and prediction of microbial shifts in coupled catalysis and biodegradation of 1,4-dioxane and co-contaminants

Microbial community dynamics were characterized following combined catalysis and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Although a few specific bacterial taxa are capable of removing 1,4-dioxane and individual CVOCs, many microorganisms are inhibited when these contaminants are present in mixtures. Chemical catalysis by tungstated zirconia (WO_x/ZrO₂) and hydrogen peroxide (H₂O₂) as a non-selective treatment was designed to achieve nearly 20% 1,4-dioxane and over 60% trichloroethene and 50% dichloroethene removals. Post-catalysis, bioaugmentation with 1,4-dioxane metabolizing bacterial strain,Pseudonocardia dioxanivorans CB1190, removed the remaining 1,4-dioxane. The evolution of the microbial community under different conditions was time-dependent but relatively independent of the concentrations of contaminants. The compositions of microbiomes tended to be similar regardless of complex contaminant mixtures during the biodegradation phase, indicating a r-K strategy transition attributed to the shock experienced during catalysis and the subsequent incubation. The originally dominant genera Pseudomonas and Ralstonia were sensitive to catalytic oxidation, and were overwhelmed by Sphingomonas, Rhodococcus, and other catalyst-tolerant microbes, but microbes capable of biodegradation of organics thrived during the incubation. Methane metabolism, chloroalkane-, and chloroalkene degradation pathways appeared to be responsible for CVOC degradation, based on the identifications of haloacetate dehalogenases, 2-haloacid dehalogenases, and cytochrome P450 family. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase that were in line with shifting predominant genera, confirming the deterministic processes guiding the microbial assembly. Collectively, this study demonstrated that catalysis followed by bioaugmentation is an effective treatment for 1,4-dioxane in the presence of high CVOC concentrations, and it enhanced our understanding of microbial ecological impacts resulting from abiotic-biological treatment trains. These results will be valuable for predicting treatment synergies that lead to cost savings and improve remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.

Forest gaps influence fungal community assembly in a weeping cypress forest

The forest gap crucially influences forest environments, but its effects on local fungal community assembly are not fully understood. In this study, the fungal community in a weeping cypress forest was investigated as a function of forest gap locations based on forest clearing, using amplicon sequencing of the ITS2 region. The results showed that the fungal community significantly varied with the variations in soil properties related to gap location. Deterministic processes played pivotal roles in fungal community assembly, which was mainly driven by the temperature, moisture, available nitrogen, and microbial carbon in soil. Beta diversity of the fungal community increased from the gap center to the closed canopy. The relative abundances of dominant orders such as Microascales, Sordariales, and Chaetothyriales regularly varied as a function of gap location, and they were potential indicators for different gap locations. Based on network analysis, gap locations caused distinct co-occurrence patterns of fungal communities. This study shed light on the roles of forest gaps in the assembly of local fungal communities and provided additional strategies to manage forest ecosystems.

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river

Although the influence of microbial community assembly processes on aquatic ecosystem function and biodiversity is well known, the processes that govern planktonic communities in human-impacted rivers remain largely unstudied. Here, we used multivariate statistics and a null model approach to test the hypothesis that environmental conditions and obstructed dispersal opportunities, dictate a deterministic community assembly for phytoplankton and bacterioplankton across contrasting hydrographic conditions in a subtropical mid-sized river (Jiulong River, southeast China). Variation partitioning analysis showed that the explanatory power of local environmental variables was larger than that of the spatial variables for both plankton communities during the dry season. During the wet season, phytoplankton community variation was mainly explained by local environmental variables, whereas the variance in bacterioplankton was explained by both environmental and spatial predictors. The null model based on Raup-Crick coefficients for both planktonic groups suggested little evidences of the stochastic processes involving dispersal and random distribution. Our results showed that hydrological change and landscape structure act together to cause divergence in communities along the river channel, thereby dictating a deterministic assembly and that selection exceeds dispersal limitation during the dry season. Therefore, to protect the ecological integrity of human-impacted rivers, watershed managers should not only consider local environmental conditions but also dispersal routes to account for the effect of regional species pool on local communities.

Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process

Temperature plays crucial roles in microbial interactions that affect the stability and performance of anaerobic digestion. In this study, the microbial interactions and their succession in the anaerobic digestion process were investigated at three levels, represented by (1) present and (2) active micro-organisms, and (3) gene expressions under a temperature gradient from 25 to 55 °C. Network topological features indicated a global variation in microbial interactions at different temperatures. The variations of microbial interactions in terms of network modularity and deterministic processes based on topological features, corresponded well with the variations of methane productions, but not with temperatures. A common successional pattern of microbial interactions was observed at different temperatures, which showed that both deterministic processes and network modularity increased over time during the digestion process. It was concluded that the increase in temperature-mediated network modularity and deterministic processes on shaping the microbial interactions improved the stability and efficiency of anaerobic digestion process.

Very Rapid and Efficient Generation of Induced Pluripotent Stem Cells from Mouse Pre-B Cells

One of the major obstacles in generating induced pluripotent stem (iPS) cells suitable for therapeutic application is the low efficiency of the process and the long time required, with many iPS lines acquiring genomic aberrations. In this chapter we describe a highly efficient iPS reprogramming system based on the transient expression in pre-B cells of the transcription factor C/EBPα, followed by the induction of the four Yamanaka factors (OSKM). In addition, the process is very rapid, yielding Oct4 positive cells within 2 days and Nanog-positive iPS cell colonies within a week.