Beta Diversity Of Communities Research Articles

Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi

Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.

Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs.

Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.

Declining salinity and increasing temperature reduce the diversity and resilience of benthic diatoms.

Climate change will modify the marine ecosystem in several ways, but the effects of changing climate on benthic diatoms, which are one of the most important photosynthesizing organism groups in benthic habitats, are poorly studied. We conducted a mesocosm experiment to investigate the effects of increasing temperature and decreasing salinity on the taxonomic and functional diversity of benthic diatoms. We showed that decreasing salinity affects the taxonomic and functional composition of communities, and the threshold salinity for community composition is ~5. This indicates that when climate change leads to decreasing salinity in brackish systems, the most pronounced changes in communities occur in areas where salinity decreases from >5 to <5. We also showed that both increasing temperature and decreasing salinity exert stress on communities and, hence, lead to the decrease of the alpha and beta diversity of communities. This indicates that climate change reduces the size of the species pool of diatoms. Our results show that, along with the changing climate, we can expect benthic diatom communities to become less diverse and less resilient.

Conceptualizing the Role of the Microbiome as a Mediator and Modifier in Environmental Health Studies: A Scoping Review of Studies of Triclosan and the Microbiome.

Triclosan is an endocrine-disrupting antimicrobial additive that is suspected of contributing to antibiotic resistance and altering the microbiome. In this scoping review, we summarize what is known about the association between triclosan exposure and the microbiome using evidence from in vivo and epidemiologic studies. Our review includes 11 rodent studies, seven fish studies, and five human studies. Evidence from animal studies suggests that triclosan decreases the diversity of the microbiome, although only one epidemiologic study agreed. Most studies suggest that triclosan alters the microbial community beta diversity, but disagree on which taxa contributed to compositional differences. Taxa in the Bacteroidetes, Firmicutes, and Proteobacteria may be more influenced by triclosan than those in other phyla. Studies on triclosan and the microbiome were scarce and were inconclusive as to the effects of triclosan on the microbiome. Additional research is needed to clarify windows of heightened susceptibility of the microbiome to triclosan. We recommend guidelines for future microbiome research in environmental health to increase comparability across studies.

Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats.

Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.

Effects of single and combined contamination of total petroleum hydrocarbons and heavy metals on soil microecosystems: Insights into bacterial diversity, assembly, and ecological function

Deciphering the impact of single and combined contamination of total petroleum hydrocarbons (TPH) and heavy metals on soil microecosystems is essential for the remediation of contaminated habitats, yet it remains incompletely understood. In this study, we employed high-throughput sequencing to investigate the impact of single TPH contamination, single metal contamination, and their co-contamination on soil microbial diversity, assembly mechanisms, composition, ecological function, and resistome. Our results revealed that contamination led to a reduction in alpha diversity, with single contamination displaying lower diversity compared to co-contamination, depending on the concentration of pollutants. Community beta diversity was primarily driven by turnover rather than nestedness, and narrower ecological niches were detected under pollution conditions. The neutral community model suggested that homogenizing dispersal played a significant role in the community assembly process under single TPH or co-contamination, while homogeneous selection dominated under heavy metals pollution. Procrustes analysis demonstrated a correlation between community composition and functional divergence, while Mantel tests linked this divergence to concentrations of Cr, Cr6+, Pb, and TPH. Interestingly, soils co-polluted with TPH and heavy metals exhibited similar genera, community functions, and resistomes as soils contaminated with only metals, highlighting the significant impact of heavy metals. Ecological functions related to carbon (C), nitrogen (N), and sulfur (S) cycles were enhanced under TPH pollution but impaired under heavy metals stress. These findings enhance our understanding of soil microecosystems subjected to TPH, heavy metals, and their co-contamination, and carry significant implications for environmental microecology and pollutant risk assessment.

Biodegradability of bacterial cellulose polymer below the soil and its effects on soil bacteria diversity

The increasing demand for sustainable materials has led to a surge in research on biodegradable polymers. This study evaluated the weight and visual changes of bacterial cellulose (BC) polymers and nylon membranes during an eight-week biodegradation study below soil. Scanning electron microscope (SEM) images were taken to investigate morphological changes from decomposition. Changes in soil microbial communities and the relationship between microbial abundance and BC biodegradation were investigated. BC was produced from the fermentation of coffee kombucha using 15 % d-dextrose C6H12O6 (DE) as the nutrient carbohydrate substrate. BCs were purified with 0.5 mol/L aqueous NaOH solution and 1.5 % (v/v) aqueous NaOCl and then freeze-dried. The biodegradation study was conducted using seedling pots and nylon membrane filters inside a greenhouse over eight weeks, with sample points taken at various intervals. Soil characteristics such as pH, nutrient content, texture, organic matter, and soil moisture were analyzed. Results showed that BC polymers underwent significant weight losses and visual decomposition, while nylon membranes did not show any weight or visual losses. Approximately 75 % of the BC polymers were decomposed by the end of the study. Fatty acid methyl ester (FAMEs) analysis showed increased microbial absolute abundance (nmol/g) for BC treatments over biodegradation time. FAMEs principal component analysis (PCA) ordination plots showed the relative abundance of fungi increased in BC microbial communities suggesting fungi's attraction to cellulose. Soil bacterial DNA analysis revealed the dominance of Proteobacteria for all treatments. PCA plots and Faith-pd index Alpha Diversity results showed significant bacterial community variations for week 2 of the biodegradation study compared to the other weeks. Adonis microbial community Beta Diversity analysis showed significant differences between treatments (p = 0.001). PCA plots also showed a slight differentiation of the bacterial communities with BC compared to bacterial communities with nylon and soil (control). This study confirms that BC is easily decomposed in soil and that its biodegradability is likely driven by fungal communities.

Disentangling the relative importance of precipitation, biocrust succession, and shrub cover in mediating soil phoD-harbouring communities and organic phosphorus mineralisation

Biological soil crusts (biocrusts) are crucial components of dryland ecosystems worldwide; however, their roles in phosphorus (P) transformation and associated functional communities have received less scientific attention compared with carbon (C) and nitrogen (N) cycling. Currently, little is known about the relative importance of precipitation, biocrust succession, and shrub cover in mediating soil P transformation. Here, we conducted a broad field survey across deserts in Northern China to investigate the roles of these factors in soil organic P (Po) mineralisation. We examined various P mineralisation parameters, including soil C:P ratio, soil Po content, bioavailable P, alkaline phosphatase (ALP)-encoding gene phoD abundance, and ALP activity. Additionally, we investigated the diversity and composition of soil phoD-harbouring communities and their relationships with Po mineralisation. Overall, the P mineralisation parameters increased with biocrust succession, and their responses to precipitation levels varied and were contingent upon the biocrust successional stages, while less significant differences were observed between the presence and absence of shrub cover. Most P mineralisation parameters were positively correlated within individual deserts or across all deserts studied. Moreover, the beta diversity, rather than the alpha diversity, of soil phoD-harbouring communities predominantly drove Po mineralisation. The abundance of certain genera (Actinoplanes and Micromonospora) that were relatively less dominant but showed significant positive correlations with P mineralisation parameters. By highlighting biocrust succession as the key determinant of soil Po mineralisation, the significance of precipitation and biocrust succession on phoD-harbouring communities, as well as the prevalence of community beta diversity in driving soil Po mineralisation, this study provides novel insights into the mechanisms underlying the transformation of Po into bioavailable P in biocrust systems.

Ecological trends in moth communities (Geometridae, Lepidoptera) along a complete rainforest elevation gradient in Papua New Guinea

Abstract The tropical rainforest elevation gradients, extending from lowlands to treeline, often represent global maxima of biodiversity and are models for community studies. We surveyed geometrid moths along a complete rainforest gradient from 200 to 3700 m asl. in Papua New Guinea. The 16,424 moths collected with light traps represented 1102 species, a high diversity for such system. We demonstrated the importance of molecular data for taxonomy as COI sequences (DNA barcodes) changed the definition of 19% of morphological species. The abundance of geometrids did not change with elevation while their species richness peaked at 1200 m asl. The mid‐elevation diversity peak is a common, but poorly understood, pattern for geometrids. It was best explained by the species richness of the vegetation. At the same time, the community was exposed to opposing trends in abiotic favourability (decreasing temperature) and biotic favourability (decreasing predation by ants, birds and bats) with elevation, potentially contributing to such unimodal trends in species richness. Beta diversity of communities separated by 500 m elevation increased with increasing elevation, reflecting decreasing mean elevational range of species—a pattern opposite to that expected under the Rapoport's rule. The total number of species along the elevation gradient corresponded to 280% of the highest local community diversity. This enrichment of species underscores the key role of long elevational gradients in maintaining high regional diversity and makes them a conservation priority, especially as they also allow for redistribution of species in response to climate change.

Partitioning beta diversity of dry and hot valley vegetation in the Nujiang River in Southwest China

The formation and continued maintenance of beta diversity are essential factors contributing to the effective conservation of plant community biodiversity and sustainable development of ecosystem functions. While it is widely acknowledged that two different patterns, including turnover and nestedness, strongly influence plant community beta diversity, their relative importance in the unique dry and hot valleys of Southwest China is yet to be fully understood. For this study, we established a 100 km belt transect in the Nujiang dry and hot valley of Southwest China and conducted community investigations. The calculations of species and phylogenetic beta diversity composition patterns allowed us to explore the relative importance of environmental and dispersal limitations in terms of their contributions to beta diversity. The findings indicated that in the Nujiang dry and hot valley of Northwest Yunnan, species and phylogenetic beta diversity in the plant communities were mainly composed of the turnover component. The values of phylogenetic beta diversity and its turnover components were lower than those of species beta diversity. Both environmental and dispersal limitations played a role in partitioning beta diversity in the region, with environmental limitations being more dominant than dispersal limitations. The analysis of specific environmental factors revealed that climate factors, such as mean annual precipitation and Hargreaves reference evaporation, and soil factors, such as pH, were the primary drivers of species and phylogenetic beta diversity in the region. In addition, we observed that various limiting environmental factors related to the growth and development of different life forms existed within the dry and hot valley communities. The study highlighted the potential benefits of establishing conservation reserves featuring multiple dominant shrub species in the Nujiang dry and hot valley of Southwest China for the protection of the vegetation. The findings demonstrated that environmental factors, particularly hydrothermal conditions, played a significant role in constraining the maintenance of beta diversity in plant communities in the dry and hot valley region at a regional scale, given the geological history and environmental changes that have occurred over time.

Regenerated woody plants influence soil microbial communities in a subtropical forest

Forests are critical for supporting multiple ecosystem services such as climate change mitigation. Microbial diversity in soil provides important functions to maintain and regenerate forest ecosystems, and yet a critical knowledge gap remains in identifying the linkage between attributes of regenerated woody plant (RWP) communities and the diversity patterns of soil microbial communities in subtropical plantations. Here, we investigated the changes in soil microbial communities and plant traits in a nine hectare Chinese fir (Cunninghamia lanceolata; CF) plantation to assess how non-planted RWP communities regulate soil bacterial and fungal diversity, and further explore the potential mechanisms that structure their interaction. Our study revealed that soil bacterial richness was positively associated with RWP richness, whereas soil fungal richness was negatively associated with RWP basal area. Meanwhile, RWP richness was positively correlated with ectomycorrhizal (ECM) fungal richness but negatively correlated with the richness of both pathogenic and saprotrophic fungi, suggesting that the RWP-fungal richness relationship was trophic guild-specific. Soil microbial community beta diversity (i.e., dissimilarity in community composition) was strongly coupled with both RWP beta diversity and the heterogeneity of RWP basal area. Our study highlights the importance of community-level RWP plant attributes for the regulation of microbial biodiversity in plantation systems, which should be considered in forest management programs in the future.

Beta Diversity of Plant Communities in Relation to Soil C:N:P Stoichiometry across 150 Years of Vegetation Restoration in a Temperate Zone

Natural solutions by which humans can overcome challenges have been severely hampered by biodiversity losses. It is essential to understand the key natural variables that influence changes in community diversity to maintain ecosystem function. The Ziwuling area has a natural recovery succession history of 150 years. Therefore, a survey was conducted to compare species composition characteristics across different vegetation recovery stages while also providing a phylogenetic and taxonomic response to the correlation between beta diversity and soil stoichiometry. The results showed that beta diversity and endemic plants had a similar single-peak temporal pattern. Soil organic carbon (SOC) accumulation was significantly positively correlated with total nitrogen (TN) and was also negatively correlated with total phosphorus (TP). Overall, soil TN, time since vegetation restoration (TVR in years), and W-SS (endemic woody plants at each stage) were able to explain 94.3% of the total variation in beta diversity. Temperate species such as Carex lanceolata, Lespedeza bicolor, and Sophora davidii are the basis for community construction. Community beta diversity patterns are the result of a mixture of ecological (e.g., climate patterns and soil nutrients) and evolutionary processes. This study combined plant resource needs with how they respond to natural recovery times in order to provide useful knowledge to protect biodiversity, the nutrient cycle, and the function of restoration ecology.

Drivers of community assembly change during succession in wood-decomposing beetle communities.

The patterns of successional change of decomposer communities is unique in that resource availability predictably decreases as decomposition proceeds. Saproxylic (i.e. deadwood-dependent) beetles are a highly diverse and functionally important decomposer group, and their community composition is affected by both deadwood characteristics and other environmental factors. Understanding how communities change with faunal succession through the decomposition process is important as this process influences terrestrial carbon dynamics. Here, we evaluate how beta-diversity of saproxylic beetle communities change with succession, as well as the effects of different major drivers of beta-diversity, such as deadwood tree species, spatial distance between locations, climate and forest structure. We studied spatial beta-diversity (i.e. dissimilarity of species composition between deadwood logs in the same year) of saproxylic beetle communities over 8 years of wood decomposition. Our study included 379 experimental deadwood logs comprising 13 different tree species in 30 forest stands in Germany. We hypothesized that the effects of tree species dissimilarity, measured by phylogenetic distance, and climate on beta-diversity decrease over time, while the effects of spatial distance between logs and forest structure increase. Observed beta-diversity of saproxylic beetle communities increased over time, whereas standardized effects sizes (SES; based on null models) of beta-diversity decreased indicating higher beta-diversity than expected during early years. Beta-diversity increased with increasing phylogenetic distance between tree species and spatial distance among regions, and to a lesser extent with spatial distance within regions and differences in climate and forest structure. Whereas effects of space, climate and forest structure were constant over time, the effect of phylogenetic distance decreased. Our results show that the strength of the different drivers of saproxylic beetle community beta-diversity changes along deadwood succession. Beta-diversity of early decay communities was strongly associated with differences among tree species. Although this effect decreased over time, beta-diversity remained high throughout succession. Possible explanations for this pattern include differences in decomposition rates and fungal communities between logs or the priority effect of early successional communities. Our results suggest that saproxylic beetle diversity can be enhanced by promoting forests with diverse tree communities and structures.

Soil bacterial community response to cover crop introduction in a wheat-based dryland cropping system

The incorporation of cover crops into cropping systems is important for enhancing soil health in agricultural systems. Soil microbes contribute to soil health by supplying key nutrients and providing protection against plant pests, diseases, and abiotic stress. While research has demonstrated the connection between cover crops and the soil microbiology, less is known regarding the impact of cover crops on the soil microbial community in semi-arid regions of the Northern Great Plains. Our objectives were to evaluate changes in the soil bacterial community composition and community networks in wheat grown after multi-species cover crops. Cover crops were compared to continuous cropping and crop/fallow systems and the effects of cover crop termination methods were also evaluated. Cover crops consisted of a cool season multispecies mix, mid-season multispecies mix, and a warm season multispecies mix, which were grown in rotation with winter wheat. A continuous cropping (wheat/barley) and wheat/fallow system were also included along with cover crop termination by grazing, herbicide application, and haying. Cover crop treatments and termination methods had no significant impact on microbial community alpha diversity. Cover crop termination methods also had no significant impact on microbial community beta diversity. Families belonging to the phyla Actinobacteria, Bacterioidota, and Proteobacteria were more abundant in the cool season cover crop treatment compared to the warm season cover crop treatment. Co-occurrence network analysis indicated that incorporation of cool season cover crops or mid-season mixes in a wheat-based cropping system led to greater complexity and connectivity within these microbial networks compared to the other treatments which suggests these communities may be more resilient to environmental disturbances.

Adding an essential oil blend to the diet of juvenile Nile tilapia improves growth and alters the gut microbiota

In aquaculture, essential oils are considered promising supplements that can improve productive performance and modulate the fish's microbiota. Here we investigate how a blend of essential oils (carvacrol + thymol + cinnamaldehyde acid) affects the productive performance and the intestinal microbiota of juvenile Nile tilapia (Oreochromis niloticus, Thai strain). All fish were randomly distributed into 20 multifilament tanks (10-mm mesh and 2.4 m3 capacity). The experimental design comprised four treatments and five repetitions, with 20 individuals per experimental unit, for 60 days. Four diets were evaluated with increasing levels of essential oils (control and 3.3, 6.7, and 10 g kg−1 diet). Supplementation with 3.3 g kg−1 of essential oils improved growth performance compared to the control group. However, no differences were detected among the essential oil-supplemented groups (6.7 and 10 g kg−1). Survival was not different among the four groups. Using a Linear Response Plateau (LRP) model, we calculated maximum levels of 3.4, 3.5, 3.5 and 3.2 g kg−1 of the essential oils blend for final weight, weight gain, daily weight gain, and feed conversion, respectively. Verrucomicrobia, Firmicutes, Bacteroidetes, and Proteobacteria accounted for a high proportion of the species observed in tilapia's gut microbiota in the control and essential oil-supplemented groups. In both treatments, Candidatus xiphinematobacter (Verrucomicrobia) and Cetobacterium (Fusobacteria) were most predominant at the genus level. Cetobacterium somerae and Lactobacillus zeae were the most abundant species. At the species level, the Shannon index diversity value was higher in the control group than in the essential oil-supplemented groups (P = 0.046719; t = 2.0586). The bacterial community beta diversity analysis revealed an effect of diet on the tilapia's gut microbiota, demonstrating a distinct grouping among treatments. Linear discriminant analysis (LDA) associated with effect size (LEfSe) identified that microbiota's differential abundance was significant when comparing the control group and the 3.3 g kg−1 essential oil-supplemented group. The genera Candidatus xiphinematobacter, Staphylococcus, Caldilinea, and Synechococcus were more abundant in the microbiota of essential oil-fed juvenile Nile tilapia the control group. Pseudomonas, Acinetobacter, Enterococcus, and Lactobacillus were more predominant in the microbiota of fish from the control group. In conclusion, dietary the carvacrol + thymol + cinnamaldehyde acid blend (3.3 g kg−1) increased the growth performance and modulated the gut microbiota of juvenile Nile tilapia.

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

Bacterioplankton Community Profiling of the Surface Waters of Kuwait

The marine waters of Kuwait are highly dynamic and strongly influenced by extreme environmental conditions and high levels of anthropogenic activities. This study explored the bacterioplankton community composition and diversity in Kuwait Bay and at four offshore sites close to urbanized coastal areas during two seasons, autumn (October) and spring (April). 16S rRNA amplicon sequencing detected higher bacterial diversity and richness in spring than in autumn. Also, bacterial community beta diversity revealed a significant seasonal partitioning between the two sampling periods but no clear spatial variation could be depicted. Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, Flavobacteriia, and Acidimicrobiia dominated the seasonal samples, and SARII clade Ia, SARII clade II, Synechococcus, and SUP05 cluster were among the most abundant taxa in the seasonal samples. However, the strong temporal shift in bacterial community composition was related to Synechococcus abundance. The prevailing physicochemical parameters displayed a significant influence on the bacterioplankton community composition, which was mainly driven by shifts in temperature and nutrient inputs. Furthermore, functional prediction by PICRUSt analysis revealed a relatively stable conserved functional profile in Kuwait’s waters. However, functional genes related to membrane transport were enriched in eutrophic spring waters, while photosynthetic genes were enriched in autumn. Our results provide in-depth insights into the temporal and spatial variations of bacterioplankton dynamics in Kuwait waters and highlight the strong seasonal influence of natural and anthropogenic stressors on their composition and predicted functional capabilities.

Megathyrsus maximus and Brachiaria decumbens improve soil characteristics and select promising rhizobacteria during rhizoremediation of petroleum hydrocarbons

Brachiaria decumbens and Megathyrsus maximus are promising grass species for the phytoremediation of soils contaminated with petroleum hydrocarbons (PHC). However, little is known about their root-associated microbiome, which is crucial for PHC degradation and plant health. Here, 16s rRNA amplicon sequencing was implemented over one year to characterize the rhizosphere bacterial communities of these two plants when growing in soil contaminated with PHC. PHC concentration and soil physicochemical parameters were monitored to analyze their interplay with the microbiome. Overall, both plants significantly increased soil fertility parameters compared to the initial soil. Specifically, porosity increased from 30.2 to 51.8; available phosphorus (AP) from 0.10 to 7.68 mg/kg; and cation exchange capacity (CEC) from 1.82 to 6.23 meq/100 g. The diversity of bacterial communities was influenced by the plants and the rhizosphere community beta-diversity was more related with AP and pH changes than with PHC concentration. M. maximus treatment showed the fastest removal of PHC (on average 23.38% less PHC compared to initial levels) at 3 months and the genera Ohtaekwangia, Luteolibacter and Ellin6067 were significantly more abundant in M. maximus’ rhizosphere compared to the other plant and the control. Additionally, genera with known plant growth promotion characteristics and PHC degradation capacity were identified to be associated with the plants and these can be targeted in future studies to confirm their role and utility as biostimulants, allowing the optimization of phytoremediation with these grasses.

Rhizosphere Microbial Community Diversity and Function Analysis of Cut Chrysanthemum During Continuous Monocropping.

As an ornamental flower crop, the long-term continuous monocropping of cut chrysanthemum causes frequent occurrence of diseases, seriously affecting the quality of cut chrysanthemum. The rhizosphere microbial community plays an important role in maintaining the healthy growth of plants, whereas the composition and dynamics of rhizosphere microbial community under continuous monocropping of cut chrysanthemum have not been fully revealed. In this study, the Illumina MiSeq high-throughput sequencing platform was used to monitor the dynamic changes of rhizosphere microbial communities in four varieties of cut chrysanthemum during 0–3 years of monocropping, and the soil physicochemical properties were also determined. Results showed that continuous monocropping significantly increased the fungal community richness and altered the profiles of the bacterial and fungal communities, leading to variation of community beta-diversity. With the increase of continuous cropping time, biocontrol bacteria decreased, while some plant pathogenic fungi were enriched in the rhizosphere of cut chrysanthemum. FAPROTAX-based functional prediction showed that the abundance of gene related to nitrogen and sulfur metabolism and chitin lysis was reduced in the rhizosphere of cut chrysanthemum. FUNGuild-based fungal function prediction showed that plant pathogenic fungal taxa were increasing in the rhizosphere of cut chrysanthemum, mainly Acremonium, Plectosphaerellaceae, Fusarium, and Cladosporium. Continuous cropping also reduced the content of ammonium nitrogen and increased soil salinity, resulting in deterioration of soil physical and chemical properties, which, together with the transformation of rhizosphere microbial community, became part of the reasons for the continuous cropping obstacle of cut chrysanthemum.

Long Term Influence of Fertility and Rotation on Soil Nitrification Potential and Nitrifier Communities

The agricultural imprints on soil microbial processes manifest at various timescales, leaving many temporal patterns to present slowly. Unfortunately, the lack of long-term continuous agricultural field sites in North America has left gaps in our understanding of agricultural management on biogeochemical processes and their controlling microbiota. Nitrification, ammonium oxidation by bacteria and archaea, is a critical control point in terrestrial nitrogen fluxes by oxidizing cationic ammonium to anionic nitrate, promoting nitrate leaching. Moreover, nitrous oxide is produced during nitrification, contributing to massive nitrous oxide emissions from fertilized agroecosystems. Nitrification is sensitive to many macro and micro-ecological filters, as nitrifiers are obligate aerobes and are sensitive to numerous non-growth substrates and metal ions. This study sought to understand the long-term implications of various rotation and fertilizer regimes on nitrification potential and nitrifying bacterial communities in the Morrow Plots (Urbana, IL). The Morrow Plots was established in 1876 and are the longest continuous field experiments in North America, making it the only site in America capable of assessing the impact of over 140 years of agricultural management on nitrification. The Morrow Plots contrasts fertilizer (manure, inorganic, unfertilized) and rotation (continuous corn, corn-soy, corn-oat alfalfa), allowing us to explore how conventional vs. regenerative agriculture practices impact nitrifier communities. The results of this study suggest that fertilizer and rotation interact to promote distinct bacterial nitrifier communities. Nitrification potential is highest in manure corn-oat-alfalfa plots, suggesting ammonium availability is not solely responsible for active nitrifier communities. Various soil chemical variables, like CEC, Mg, and Ca, significantly influenced nitrifier community beta-diversity, using 16S rRNA amplicon sequencing, suggesting long-term accumulation of specific cations diverge microbial community assembly. While this study only uses nitrification potential enzyme activity instead of isotope analyses, it sheds light on the importance of various physiochemical drivers on nitrification potential and communities. The results support the need for a more precise exploration of the mechanisms controlling field-scale nitrification rates over large temporal scales. Put together, this study supports the importance of long-term field sites for understanding agricultural manipulations of microbial biogeochemical cycling and sheds light on the micronutrients influencing nitrifier communities and potential activity.