Variation In Communities Research Articles

Plant and soil microbial community assembly processes across urban vacant lots

AbstractQuestionsNumerous studies on community assembly processes have been conducted in natural ecosystems. However, we know little about community assembly processes in human‐dominated urban ecosystems. Here, we asked: (1) how are the composition and functional diversity of native and exotic plant species shaped by local environment and landscape factors across urban vacant lots; and (2) how is microbial (bacterial and fungal) community composition influenced by the local environment, landscape factors, and plant species composition across urban vacant lots?LocationWe investigated 69 urban vacant lots in Yokohama, Japan.MethodsBy using a variation partitioning approach, we examined the relative importance of local environmental and landscape factors (including land use and spatial structure) in explaining variation in plant species composition and functional diversity of native or exotic species. We also explored the relative importance of local environmental and landscape factors, and plant species composition in explaining variation in microbial community composition.ResultsThe spatial structure of vacant lots determined the species composition and functional diversity of plant communities, suggesting that plant community assembly is determined by dispersal limitation. However, the functional diversity of the exotic species varied randomly, which reduced the relative importance of the spatial structure of vacant lots. Plant species composition as well as the spatial structure of vacant lots were the important drivers of the composition of soil microbial communities, despite a higher proportion of unexplained variation in their composition. Finally, we found an essential contribution of earthmoving methods in explaining the variations in both plant and microbial community composition.ConclusionPlant and microbial community composition would be largely determined by dispersal limitation across urban vacant lots. Understanding urban community assembly is critical for predicting plant and microbial communities that play an essential role in regulating urban ecosystem functioning and services.

Leachate derived humic-like substances drive the variation in microbial communities in landfill-affected groundwater

Landfills are commonly used for waste disposal in many countries, and pose a significant threat of groundwater contamination. Dissolved organic matter (DOM) plays a crucial role as a carbon and energy source, supporting the growth and activity of microorganisms. However, the changes in the DOM signature and microbial community composition in landfill-affected groundwater and their bidirectional relationships remain inadequately explored. Herein, we showed that DOM originating from more recent landfills mainly comprises microbially produced substances resembling tryptophan and tyrosine. Conversely, DOM originating from older landfills predominantly comprises fulvic-like and humic-like compounds. Leachate leakage increases microbial diversity and richness and facilitates the transfer of foreign bacteria from landfills to groundwater, thereby increasing the vulnerability of the microbial ecosystem in groundwater. Deterministic processes dominated the assembly of the groundwater microbial community, while stochastic processes accounted for an increased proportion of the microbial community in the old landfills. The dominant phyla observed in groundwater were Proteobacteria, Bacteroidota, and Actinobacteriota, and humic-like substances play a crucial role in driving the variation in microbial communities in landfill-affected groundwater. Predictions using PICRUSt2 suggested significant associations between various metabolic pathways and microbial communities, with the Kyoto Encyclopedia of Genes and Genomes pathway “Metabolism” being the most predominant. The findings contribute to advancing our understanding of the transformation of DOM and its interplay with microbial communities and can serve as a scientific reference for decision-making regarding groundwater pollution monitoring and remediation.

Spatial and diel variations of bacterioplankton and pico-nanoeukaryote communities and potential biotic interactions during macroalgal blooms

We investigated spatial heterogeneity and diel variations in bacterioplankton and pico-nanoeukaryote communities, and potential biotic interactions at the extinction stage of the Ulva prolifera bloom in the Jiaozhou Bay, Yellow Sea. It was found that the presence of Ulva canopies significantly promoted the cell abundance of heterotrophic bacteria, raised evenness, and altered the community structure of bacterioplankton. A diel pattern was solely significant for pico-nanoeukaryote community structure. >50 % of variation in the heterotrophic bacterial abundance was accounted for by the ratio of Bacteroidota to Firmicutes, and dissolved organic nitrogen effectively explained the variations in cell abundances of phytoplankton populations. The factors representing biotic interactions frequently contributed substantially more than environmental factors in explaining the variations in diversity and community structure of both bacterioplankton and pico-nanoeukaryotes. There were higher proportions of eukaryotic pathogens compared to other marine systems, suggesting a higher ecological risk associated with the Ulva blooms.

Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering.

Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.

Variations in the Odonata Assemblages: How Do the Dry Season and Water Bodies Influence Them?

Diverse abiotic and biotic factors drive the ecological variation of communities across spatial and temporal dimensions. Within the Amazonian landscape, various freshwater environments exhibit distinct physicochemical characteristics. Thus, our study delved into the fluctuations of Odonata assemblages amidst distinct water bodies within Amazonia, encompassing two distinct climatic seasons. Comparative analysis was conducted on Odonata species diversity and assemblage composition across a blackwater pond, a lake, and a stream, spanning the initiation and culmination of the dry season in the southwestern Amazon region in Peru. Our methodology involved capturing adult Odonata using entomological nets on three separate occasions between 11:00 and 14:00h for each water body in May (beginning of the dry season) and October (end of the dry season) of 2018. We also evaluated the influence of temperature, precipitation, and percent cloud cover on the abundance and richness of adult Odonata. Species richness and composition differed among the three water bodies in both periods of the dry season. No effect of the dry season periods on species richness and abundance was observed. However, except in the oxbow lake, the more abundant species were substituted to the end of the dry season. Our study highlights the influence of water body types on Odonata species diversity and composition. The effects of the sampling period during the dry season may not be immediately apparent in conventional diversity metrics, such as species richness and abundance. Instead, its effects manifest predominantly in the relative abundance of the species that compose these assemblages.

Thresholds of Nitrogen and Phosphorus Input Substantially Alter Arbuscular Mycorrhizal Fungal Communities and Wheat Yield in Dryland Farmland.

Arbuscular mycorrhizal (AM) fungi are essential for preserving the multifunctionality of ecosystems. The nitrogen (N)/phosphorus (P) threshold that causes notable variations in the AM fungus community of the soil and plant productivity is still unclear. Herein, a long-term (18 years) field experiment with five N and five P fertilizer levels was conducted to investigate the change patterns of soil AM fungus, multifunctionality, and wheat yield. High-N and -P fertilizer inputs did not considerably increase the wheat yield. In the AM fungal network, a statistically significant positive correlation was observed between ecosystem multifunctionality and the biodiversity of two primary ecological clusters (N: Module #0 and P: Module #3). Furthermore, fertilizer input thresholds for N (92-160 kg ha-1) and P (78-100 kg ha-1) significantly altered the AM fungal community, soil characteristics, and plant productivity. Our study provided a basis for reduced N and P fertilizer application and sustainable agricultural development from the aspect of soil AM fungi.

Emergence and spread patterns of antibiotic resistance genes during cultivating aerobic granular sludge under different feeding modes

Aerobic granular sludge (AGS) technology, which is a promising approach for wastewater treatment, encounters challenges associated with antibiotic resistance genes (ARGs) in biological treatment systems. This study investigates the dynamics of ARGs during AGS cultivation under anaerobic plug-flow (APM), anaerobic mixed-flow (AMM), and aerobic feeding mode (AFM). Significant differences (P < 0.05) are observed in the shifts of ARGs among these modes. The abundance of ARGs notably increases under all modes, with AMM exhibiting a lower average relative abundance (0.063 ± 0.025) compared to that of APM (0.148 ± 0.061) and AFM (0.147 ± 0.047). The observed variations in bacterial communities and the co-selection of ARGs among the feeding modes are likely influential factors contributing to the documented variations of ARGs. Furthermore, the study identifies tnpA and intl1 as key contributors to horizontal gene transfer (HGT) during APM and AFM operations. Additionally, a heightened level of HGT is observed in both APM and AFM, with a larger potential host range (12 hosts each) harboring ARGs, in contrast to AMM (4 hosts). The study highlights the pivotal role played by distinct bacterial communities and the co-selection of ARGs in ARG variations across feeding modes. AMM emerges as an effective strategy for mitigating ARG proliferation, thereby enhancing the safety and sustainability of AGS technology in wastewater treatment.

The Role of Gut Microbiota and Its Metabolites in Patients with Heart Failure.

Heart failure (HF) is a significant health concern; early detection and prevention are crucial. Recent studies suggest that the gut microbiota and its metabolites may influence HF development and risk factors. We explored this relationship by examining changes in gut microbiota composition and metabolite levels in HF patients. HF patients often exhibit decreased alpha and beta diversity compared to controls, suggesting lower bacterial richness and community variation. Changes in specific bacterial phyla were observed, with decreases in Firmicutes (e.g., Ruminococcus) and Bacteroidetes (e.g., Prevotella) and increases in Proteobacteria (e.g., Escherichia, Shigella, and Klebsiella) and Actinobacteria. Gut-microbiota-related metabolites have been identified, potentially affecting various body systems, including the cardiovascular system. Among these are short-chain fatty acids (SCFAs), betaine, trimethylamine N-oxide (TMAO), phenylalanine, tryptophan-kynurenine, and phenylacetylgutamine (PAGIn). Although SCFAs positively affect our organisms, patients with HF have been observed to experience a decline in bacteria responsible for producing these chemical compounds. There have been indications of possible links between betaine, TMAO, phenylalanine, tryptophan-kynurenine, PAGIn, and heart failure. TMAO and phenylalanine, in particular, show promise as potential prognostic factors. However, their clinical significance has not yet been thoroughly evaluated and requires further investigation.

Mitigated N2O emissions from submerged-plant-covered aquatic ecosystems on the Changjiang River Delta

Submerged plants affect nitrogen cycling in aquatic ecosystems. However, whether and how submerged plants change nitrous oxide (N2O) production mechanism and emissions flux remains controversial. Current research primarily focuses on the feedback from N2O release to variation of substrate level and microbial communities. It is deficient in connecting the relative contribution of individual N2O production processes (i.e., the N2O partition). Here, we attempted to offer a comprehensive understanding of the N2O mitigation mechanism in aquatic ecosystems on the Changjiang River Delta according to stable isotopic techniques, metagenome-assembly genome analysis, and statistical analysis. We found that the submerged plant reduced 45 % of N2O emissions by slowing down the dissolved inorganic nitrogen conversion velocity to N2O in sediment (Vf-[DIN]sed). It was attributed to changing the N2O partition and suppressing the potential capacity of net N2O production (i.e., nor/nosZ). The dominated production processes showed a shift with increasing excess N2O. Meanwhile, distinct shift thresholds of planted and unplanted habitats reflected different mechanisms of stimulated N2O production. The hotspot zone of N2O production corresponded to high nor/nosZ and unsaturated oxygen (O2) in unplanted habitat. In contrast, planted habitat hotspot has lower nor/nosZ and supersaturated O2. O2 from photosynthesis critically impacted the activities of N2O producers and consumers. In summary, the presence of submerged plants is beneficial to mitigate N2O emissions from aquatic ecosystems.

Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season.

The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.

Human habitat modification, not apex scavenger decline, drives isotopic niche variation in a carnivore community.

Top carnivores can influence the structure of ecological communities, primarily through competition and predation; however, communities are also influenced by bottom-up forces such as anthropogenic habitat disturbance. Top carnivore declines will likely alter competitive dynamics within and amongst sympatric carnivore species. Increasing intraspecific competition is generally predicted to drive niche expansion and/or individual specialisation, while interspecific competition tends to constrain niches. Using stable isotope analysis of whiskers, we studied the effects of Tasmanian devil Sarcophilus harrisii declines upon the population- and individual-level isotopic niches of Tasmanian devils and sympatric spotted-tailed quolls Dasyurus maculatus subsp. maculatus. We investigated whether time since the onset of devil decline (a proxy for severity of decline) and landscape characteristics affected the isotopic niche breadth and overlap of devil and quoll populations. We quantified individual isotopic niche breadth for a subset of Tasmanian devils and spotted-tailed quolls and assessed whether between-site population niche variation was driven by individual-level specialisation. Tasmanian devils and spotted-tailed quolls demonstrated smaller population-level isotopic niche breadths with increasing human-modified habitat, while time since the onset of devil decline had no effect on population-level niche breadth or interspecific niche overlap. Individual isotopic niche breadths of Tasmanian devils and spotted-tailed quolls were narrower in human-modified landscapes, likely driving population isotopic niche contraction, however, the degree of individuals' specialisation relative to one another remained constant. Our results suggest that across varied landscapes, mammalian carnivore niches can be more sensitive to the bottom-up forces of anthropogenic habitat disturbance than to the top-down effects of top carnivore decline.

Temperature Mainly Determined the Seasonal Variations in Soil Faunal Communities in Semiarid Areas

The implementation of the Grain for Green Project has increased vegetation coverage and provided suitable habitats and food resources for soil fauna, thereby promoting the development of soil faunal communities. Studying seasonal variations in soil fauna communities in different vegetation areas can improve our understanding of the mechanisms that drive soil fauna recovery. We selected five typical artificially restored vegetation habitats, including Populus simonii (POS), Pinus tabulaeformis (PIT), Caragana korshinskii (CAK), Stipa bungeana (STB), and Medicago sativa (MES), and one farmland (Zea mays, FAL) habitat on the Loess Plateau. In this study, soil fauna communities and environmental factors were investigated during spring (May), summer (August), and autumn (November). Among the habitats, the STB habitat had the largest seasonal variation in soil faunal density (from 1173 ind·m−2 in May to 10,743 ind·m−2 in August), and the FAL habitat had the smallest (from 2827 ind·m−2 in August to 5550 ind·m−2 in November). Among the restored vegetation habitats, Acarina (44.89–88.56%) had the highest relative abundance of all taxa. The redundancy analysis (RDA) results showed that among the factors driving seasonal variation in soil animal communities, temperature (47.41%) was the most important, followed by precipitation (22.60%). In addition, the dominant groups, Acarina and Collembola, played an influential role in seasonal variations in soil faunal density. Temperature mainly determined the seasonal variations in soil faunal communities. Seasonal factors should be considered when conducting soil fauna research, as they contribute to biodiversity conservation and regional ecological management in the Loess Plateau.

Variation in seed-borne microbial communities of Metrosideros excelsa Sol. ex Gaertn. with consequences for germination success

ABSTRACT Seed endophytic bacteria and fungi are co-dispersed with seeds and are likely founders of the initial endophytic microbiome in developing seedlings. The effects of the seed microbiome on seedling survival and growth are of particular interest for their roles in protection against pathogens and plant resistance to environmental stress. The fungal pathogen Austropuccinia psidii (G. Winter) Beenken is the causal agent of myrtle rust, which infects more than 480 species of Myrtaceae globally and poses a severe threat to New Zealand endemic species such as Metrosideros excelsa Sol. ex Gaertn. We hypothesised that seedlings of M. excelsa may contain seed-derived microbial communities that may contribute to variation in susceptibility to A. psidii. Culture based methods were used to recover 22 species of fungi (n = 412 isolates) and 16 bacterial taxa (n = 156 isolates) from 1580 M. excelsa seeds collected from 30 trees. Our results indicate broad variation in the isolation frequency and species composition of seed-borne microorganisms among individual trees: while seeds sampled from four trees were free of culturable microorganisms, the other 26 trees accumulated up to eight culturable taxa (both bacteria and fungi) in their seeds, including some species known to be beneficial endophytes or phytopathogens. The most frequently isolated fungal species belong to genera Aureobasidium, Cladosporium, Penicillium, and Pestalotiopsis. These fungi were often isolated from seeds also containing bacteria of the genera Bacillus, Erwinia, and Methylobacterium. At the same time, seeds collected from four trees contained known plant pathogens Colletotrichum aff. fioriniae (Marcelino & Gouli) Pennycook, Neofusicoccum sp., and Robbsia aff. andropogonis (Smith) Lopes-Santos et al., which could affect seed germination. This is the first report of bacterial and fungal communities residing in seeds of endemic New Zealand trees and the potential effects of seed-borne microbiomes on germination.

Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors.

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Drivers of Macroinvertebrate Communities in Mediterranean Rivers: A Mesohabitat Approach

We investigated the relationship between benthic macroinvertebrate community attributes (richness, abundance, biodiversity, and climate-specific and resistance forms) and the physical characteristics of distinct mesohabitats (hydromorphological unit types) discretized into fast (e.g., riffles or rapids) and slow (e.g., pools or glides) flow types in four Mediterranean rivers of Spain. Key attributes of hydromorphological units, including length, width, depth, shade, substrate composition, embeddedness, abundance of aquatic vegetation, and density of woody debris, were considered. Through a comprehensive suite of multivariate analyses, we unraveled taxonomic and habitat distinctions among rivers and hydromorphological unit types, with a notable influence of spatial proximity (greater similarity within the same river basin). In slow hydromorphological units, aquatic vegetation, depth, and abundance of coarse substrate emerged as pivotal factors shaping macroinvertebrate assemblages, whereas in fast-flowing units, vegetation, substrate embeddedness, and density of woody debris were the most important. Contrary to the remaining community attributes, the studied resistance forms (absent, eggs, cocoons, and cells against desiccation and diapause) exhibited uniformity across rivers despite observed variations in macroinvertebrate communities, underscoring regional functional analogies in biological and ecological mechanisms within the investigated Mediterranean river basins. This study contributes valuable insights for anticipating the repercussions of ongoing climate change, particularly in regions where fast-flowing hydromorphological units are more susceptible to depletion during drought periods.

Childcare centre soil microbiomes are influenced by substrate type and surrounding vegetation condition

Urban development has profoundly reduced human exposure to biodiverse environments, which is linked to a rise in human disease. The ‘biodiversity hypothesis’ proposes that contact with diverse microbial communities (microbiota) benefits human health, as exposure to microbial diversity promotes immune training and regulates immune function. Soils and sandpits in urban childcare centres may provide exposure to diverse microbiota that support immunoregulation at a critical developmental stage in a child's life. However, the influence of outdoor substrate (i.e., sand vs. soil) and surrounding vegetation on these environmental microbiota in urban childcare centres remains poorly understood. Here, we used 16S rRNA amplicon sequencing to examine the variation in bacterial communities in sandpits and soils across 22 childcare centres in Adelaide, Australia, plus the impact of plant species richness and habitat condition on these bacterial communities. We show that sandpits had distinct bacterial communities and lower alpha diversity than soils. In addition, we found that plant species richness in the centres' yards and habitat condition surrounding the centres influenced the bacterial communities in soils but not sandpits. These results demonstrate that the diversity and composition of childcare centre sandpit and soil bacterial communities are shaped by substrate type, and that the soils are also shaped by the vegetation within and surrounding the centres. Accordingly, there is potential to modulate the exposure of children to health-associated bacterial communities by managing substrates and vegetation in and around childcare centres.

Forest top canopy bacterial communities are influenced by elevation and host tree traits

BackgroundThe phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce).ResultsWe profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families.ConclusionsWhile our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

The Effects of Mine Waste and Rain Water on the Structure of Bacteria Community of Paddy Soils

ABSTRACT Heavy metal contamination of soil has become one of the most important environmental problems worldwide. Heavy metals can affect growth and lead to changes in microbial community composition, which could influence the growth of crops in the soil. In this study, we conducted an experiment to investigate the distribution profile of heavy metals and bacterial communities in soil with the effects of slag and/or water on the top of the soil. Extra heavy metals, acting as selective pressure, led to the loss of sensitive taxa, with tolerant or less sensitive taxa being more abundant in the community. The results showed that the addition of slag on the top of soils did not change the diversity of bacteria but influenced the relative abundance of indigenous members in the community. Water addition, however, improved the homogeneity of the environment vertically in the soil, which consequently led to a lower variation in the bacterial community. This study mimicked the scenario of tailings and abandoned mines in nature, and aimed to study the effects of mines on the soil microbial community with the influence of precipitation on the distribution of heavy metals in the soil. With the effect of precipitation, the transportation of heavy metals in the slag may influence the local bacterial community and subsequently undermine the quality of soil for agriculture. These observations provide evidence of the effects of heavy metals on the soil around abandoned mines without any treatment. Mining causes both heavy metal and water pollution, which may lead to the accumulation of heavy metals in plants and agricultural production. Therefore, it is necessary to take care of tailings with proper procedures instead of exposing them to nature.

Beta diversity and regionalization of the western Atlantic marine biota

AbstractAimUnderstanding the factors determining marine community variations is important for biogeography and conservation. Beta diversity is a metric for mapping species composition variations between communities and regionalizing biota. Ecoregions are commonly used for regionalization, but their empirical testing has been limited. Our aim is to map marine species composition variations in the Western Atlantic, identify variables related to these variations, and regionalize areas based on community distribution. Additionally, we test whether currently proposed ecoregions represent unique biota units and specific environmental conditions.LocationWestern Atlantic Ocean.TaxonVertebrates, invertebrates and algae.MethodsWe constructed a large marine biodiversity database, including vertebrates, invertebrates, and algae, totalling over 4 million records. We used the generalized dissimilarity model (GDM) to identify variables most related to species composition variations and map beta‐diversity variations. We employed an unsupervised classifier for community regionalization. To test if the ecoregion regionalization boundaries are corroborated by species distribution data, we used the Sørensen index. To assess if ecoregions correspond to environmental units, we checked if areas had distinct environmental conditions using a PCA of 134 marine environmental variables.ResultsThe GDM explained a high variation in species composition, 61% in the complete database. Analysing vertebrates, invertebrates and algae separately also yielded relatively high results: 46%, 54%, and 33%, respectively. Coastal areas differed from open sea areas in composition. Environmental variables combined better explained beta diversity than isolated variables. The regionalization based on GDM was not congruent with ecoregion boundaries. Moreover, ecoregions showed no distinction in species composition or environmental conditions.Main ConclusionsThis study's regionalization is crucial for marine biodiversity conservation, focusing on understanding species composition patterns between coastal and open sea areas to develop tailored conservation strategies. Despite sampling limitations, the study advances marine biogeography knowledge by analysing over 4 million species records and 134 environmental variables. This comprehensive approach enhances understanding marine species distribution and diversity and aiding the development of effective conservation measures.