Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

Bacterial community profiles within the water samples of leptospirosis outbreak areas

Background

Leptospirosis is a water-related zoonotic disease. The disease is primarily transmitted from animals to humans through pathogenic Leptospira bacteria in contaminated water and soil. Rivers have a critical role in Leptospira transmissions, while co-infection potentials with other waterborne bacteria might increase the severity and death risk of the disease.

Methods

The water samples evaluated in this study were collected from four recreational forest rivers, Sungai Congkak, Sungai Lopo, Hulu Perdik, and Gunung Nuang. The samples were subjected to next-generation sequencing (NGS) for the 16S rRNA and in-depth metagenomic analysis of the bacterial communities.

Results

The water samples recorded various bacterial diversity. The samples from the Hulu Perdik and Sungai Lopo downstream sampling sites had a more significant diversity, followed by Sungai Congkak. Conversely, the upstream samples from Gunung Nuang exhibited the lowest bacterial diversity. Proteobacteria, Firmicutes, and Acidobacteria were the dominant phyla detected in downstream areas. Potential pathogenic bacteria belonging to the genera Burkholderiales and Serratia were also identified, raising concerns about co-infection possibilities. Nevertheless, Leptospira pathogenic bacteria were absent from all sites, which is attributable to its limited persistence. The bacteria might also be washed to other locations, contributing to the reduced environmental bacterial load.

Conclusion

The present study established the presence of pathogenic bacteria in the river ecosystems assessed. The findings offer valuable insights for designing strategies for preventing pathogenic bacteria environmental contamination and managing leptospirosis co-infections with other human diseases. Furthermore, closely monitoring water sample compositions with diverse approaches, including sentinel programs, wastewater-based epidemiology, and clinical surveillance, enables disease transmission and outbreak early detections. The data also provides valuable information for suitable treatments and long-term strategies for combating infectious diseases.

Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana

The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BACKGROUND

The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS

To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION

Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

Litter decomposition and nutrient release are faster under secondary forests than under Chinese fir plantations with forest development

In terrestrial ecosystems, leaf litter is the main source of nutrients returning to the soil. Understanding how litter decomposition responds to stand age is critical for improving predictions of the effects of forest age structure on nutrient availability and cycling in ecosystems. However, the changes in this critical process with stand age remain poorly understood due to the complexity and diversity of litter decomposition patterns and drivers among different stand ages. In this study, we examined the effects of stand age on litter decomposition with two well-replicated age sequences of naturally occurring secondary forests and Chinese fir (Cunninghamia lanceolata) plantations in southern China. Our results showed that the litter decomposition rates in the secondary forests were significantly higher than those in the Chinese fir plantations of the same age, except for 40-year-old forests. The litter decomposition rate of the Chinese fir initially increased and then decreased with stand age, while that of secondary forests gradually decreased. The results of a structural equation model indicated that stand age, litter quality and microbial community were the primary factors driving nutrient litter loss. Overall, these findings are helpful for understanding the effects of stand age on the litter decomposition process and nutrient cycling in plantation and secondary forest ecosystems.

Soil nutrients, enzyme activities, and bacterial communities in varied plant communities in karst rocky desertification regions in Wushan County, Southwest China

Vegetation restoration has become a common practice in karst rocky desertification (KRD) areas of southwestern China. The bacteria, which have made a connection between soil and plants, have been an important role in regulating the succession and restoration of karst vegetation. However, it is still unclear how soil bacterial communities and soil properties respond to natural vegetation restoration processes in karst areas. To address this gap, we investigated the soil nutrients, enzyme activity, and soil bacterial community among various plant communities, including farmland (FL), land with herbs only (SSI), herb-and-shrub land (SSII), woody thickets (SSIII), coniferous forest (SSIV), coniferous and broad-leaved mixed forest (SSV), and evergreen broad-leaved forest (SSVI). Our results found that SSII had the highest levels of soil organic matter, total nitrogen, available phosphorus, available nitrogen, sucrase, and β-glucosidase among all the plant communities. These results indicated that herb-and-shrub land have contributed to the rapid restoration of vegetation in KRD regions. FL exhibited the lowest levels of soil nutrients and enzyme activities, while showing the highest bacterial richness and diversity among all the plant communities. This suggested that appropriate human intervention can increase bacterial diversity and richness in the area. The predominant bacterial phylum also varied among the different plant communities, with Actinobacteria being the most abundant in SSI, SSII, SSIII, and SSIV, while Proteobacteria were the most abundant in SSV and SSVI. Furthermore, PCoA analysis demonstrated significant changes in the soil bacterial community structure, with SSI, SSII, SSIII, and SSIV had shared similar structures, while SSV and SSVI had comparable structures. As for soil characteristics, total phosphorus (TP) and total potassium (TK) were the primary factors affecting the soil bacterial community. SSV and SSVI had the most complex bacterial networks and were more stable than other groups. The genera Ktedonobacter, norank_f_Anaerolineaceae, and Vicinamibacter had the highest betweenness centrality scores and were identified as keystone genera in the co-occurrence network in KRD areas. In summary, our results have demonstrated that herb-and-shrub can promote community succession and increase soil nutrient levels in KRD regions.

The competitive strategies of poisonous weeds Elsholtzia densa Benth. on the Qinghai Tibet Plateau: Allelopathy and improving soil environment

Introduction

The competitive strategies of plants play a crucial role in their growth. Allelopathy is one of the weapons that plants use to improve their competitive advantage.

Methods

In order to explore the competitive strategy of a poisonous weed Elsholtzia densa Benth. (E. densa) on the Qinghai-Tibet Plateau (QTP), the effects of decomposing substances of E. densa on growth, root border cells (RBCs) characteristics of highland crop highland barley (Hordeum vulgare L.), and soil environment were determined.

Results

The decomposing allelopathic effect of E. densa on the germination and seedling growth of highland barley mainly occurred in the early stage of decomposing. The allelopathic effects were mainly on seed germination and root growth of highland barley. After treatment with its decomposing solution, the RBC's mucilage layer of highland barley thickened, and the RBC's activity decreased or even apoptosis compared with the control. However, only the above-ground part of the treatment group showed a significant difference. The effects of E. densa decomposed substances on the soil environment were evaluated from soil physicochemical properties and bacterial community. The results showed that soil bacteria varied greatly in the early stage of decomposion under different concentrations of E. densa. In addition, E. densa decomposing substances increased the soil nutrient content, extracellular enzyme activities, and bacterial community diversity. In the process of decomposition, the bacterial community structure changed constantly, but Actinobacteriota was always the dominant phylum.

Discussion

These results indicated that E. densa might adopt the following two strategies to help it gain an advantage in the competition: 1. Release allelochemicals that interfere with the defense function of surrounding plants and directly inhibit the growth and development of surrounding plants. 2. By changing the physical and chemical properties of soil and extracellular enzyme activity, residual plant decomposition can stimulate soil microbial activity, improve soil nutrition status, and create a more suitable soil environment for growth.

Responses of soil fungal communities and functional guilds to ~160 years of natural revegetation in the Loess Plateau of China

Natural revegetation has been widely confirmed to be an effective strategy for the restoration of degraded lands, particularly in terms of rehabilitating ecosystem productivity and soil nutrients. Yet the mechanisms of how natural revegetation influences the variabilities and drivers of soil residing fungal communities, and its downstream effects on ecosystem nutrient cycling are not well understood. For this study, we investigated changes in soil fungal communities along with ~160 years of natural revegetation in the Loess Plateau of China, employing Illumina MiSeq DNA sequencing analyses. Our results revealed that the soil fungal abundance was greatly enhanced during the later stages of revegetation. As revegetation progresses, soil fungal richness appeared first to rise and then decline at the climax Quercus liaotungensis forest stage. The fungal Shannon and Simpson diversity indexes were the lowest and highest at the climax forest stage among revegetation stages, respectively. Principal component analysis, Bray–Curtis similarity indices, and FUNGuild function prediction suggested that the composition, trophic modes, and functional groups for soil fungal communities gradually shifted along with natural revegetation. Specifically, the relative abundances of Basidiomycota, Agaricomycetes, Eurotiomycetes, and ectomycorrhizal fungi progressively increased, while that of Ascomycota, Sordariomycetes, Dothideomycetes, Tremellomycetes, saprotrophic, pathotrophic, arbuscular mycorrhizal fungi, and endophyte fungi gradually decreased along with natural revegetation, respectively. The most enriched members of Basidiomycota (e.g., Agaricomycetes, Agaricales, Cortinariaceae, Cortinarius, Sebacinales, Sebacinaceae, Tricholomataceae, Tricholoma, Russulales, and Russulaceae) were found at the climax forest stage. As important carbon (C) sources, the most enriched symbiotic fungi (particularly ectomycorrhizal fungi containing more recalcitrant compounds) can promote organic C and nitrogen (N) accumulation in soils of climax forest. However, the most abundant of saprotrophic fungi in the early stages of revegetation decreased soil organic C and N accumulation by expediting the decomposition of soil organic matter. Our results suggest that natural revegetation can effectively restore soil fungal abundance, and modify soil fungal diversity, community composition, trophic modes, and functional groups by altering plant properties (e.g., plant species richness, diversity, evenness, litter quantity and quality), quantity and quality of soil nutrient substrates, soil moisture and pH. These changes in soil fungal communities, particularly their trophic modes and functional groups along with natural revegetation, impact the accumulation and decomposition of soil C and N and potentially affect ecosystem C and N cycling in the Loess Plateau of China.

Secondary Succession in the Tropical Lowland Rainforest Reduced the Stochasticity of Soil Bacterial Communities through the Stability of Plant Communities

The effects of natural succession on plant and soil bacterial communities were previously established, but changes in plant and soil bacterial communities and their response to soil properties are not well characterized in different stages of secondary forest succession, especially in tropical regions with endemic plant species. We investigated the dynamics of plant communities, soil properties and the structure of soil bacterial communities at sites representing 33 (early successional stage), 60 (early-mid successional stage) and 73 (mid successional stage) years of secondary succession in the tropical lowland rainforest of Hainan, China, by using16S rRNA high-throughput sequencing. From the perspective of plant composition, the number of families, genera and species were increasing along with the progress of succession. Additionally, the changes in the ranking of important values along with the progress of the forest succession were consistent with the niche width calculated by the previous stage of the plant community. The results of niche overlap, Pearson’s correlation and Spearman’s rank correlation coefficients and significance indicated that in the early stage of succession, tree species did not fully utilize environmental resources. Then, as time went by, the number of negative correlations of plants in the early-mid stage was more than that in the mid stage of succession. Significant differences were found in the species richness of soil microorganisms among the three successional stages. Nutrient contents in early successional stage rainforests were less abundant than in early-mid and mid forest soils. The influence of soil nutrient concentration, particularly N and P content, on soil bacterial composition at the phylum level was larger in the early-mid stage than in the mid stage. The stochasticity of the soil bacterial community at the early successional stage of the rainforest was significantly higher than that at mid stage. Overall, as the diversity of plant communities increased, the competition decreased, the soil nutrient content changed and the stochasticity of soil bacterial communities decreased as a result of forest succession.

The Distribution and Turnover of Bacterial Communities in the Root Zone of Seven Stipa Species Across an Arid and Semi-arid Steppe

The bacterial communities of the root-zone soil are capable of regulating vital biogeochemical cycles and the succession of plant growth. Stipa as grassland constructive species is restricted by the difference features of east–west humidity and north–south heat, which shows the population substituting distribution. The distribution, turnover, and potential driving factors and ecological significance of the root-zone bacterial community along broad spatial gradients of Stipa taxa transition remain unclear. This paper investigated seven Stipa species root-zone soils based on high-throughput sequencing combined with the measurements of multiple environmental parameters in arid and semi-arid steppe. The communities of soil bacteria in root zone had considerable turnover, and some regular variations in structure along the Stipa taxa transition are largely determined by climatic factors, vegetation coverage, and pH at a regional scale. Bacterial communities had a clear Stipa population specificity, but they were more strongly affected by the main annual precipitation, which resulted in a biogeographical distribution pattern along precipitation gradient, among which Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi were the phyla that were most abundant. During the transformation of Stipa taxa from east to west, the trend of diversity shown by bacterial community in the root zone decreased first, and then increased sharply at S. breviflora, which was followed by continuous decreasing toward northwest afterwards. However, the richness and evenness showed an opposite trend, and α diversity had close association with altitude and pH. There would be specific and different bacterial taxa interactions in different Stipa species, in which S. krylovii had the simplest and most stable interaction network with the strongest resistance to the environment and S. breviflora had most complex and erratic. Moreover, the bacterial community was mainly affected by dispersal limitation at a certain period. These results are conducive to the prediction of sustainable ecosystem services and protection of microbial resources in a semi-arid grassland ecosystem.

Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China

Simple Summary

Tropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations.

Abstract

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

Orchid Root Associated Bacteria: Linchpins or Accessories?

Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake

Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).