Shifts In Bacterial Community Structure Research Articles

Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil

Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg−1 significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %–40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg−1 after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.

Shift in Bacterial Community Structure in the Biodegradation of Benzene and Toluene under Sulfate-Reducing Condition.

Groundwater contaminated by benzene and toluene is a common issue, posing a threat to the ecosystems and human health. The removal of benzene and toluene under sulfate-reducing condition is well known, but how the bacterial community shifts during this process remains unclear. This study aims to evaluate the shift in bacterial community structure during the biodegradation of benzene and toluene under sulfate-reducing condition. In this study, groundwater contaminated with benzene and toluene were collected from the field and used to construct three artificial samples: Control (benzene 50 mg/L, toluene 1.24 mg/L, sulfate 470 mg/L, and HgCl2 250 mg/L), S1 (benzene 50 mg/L, toluene 1.24 mg/L, sulfate 470 mg/L), and S2 (benzene 100 mg/L, toluene 2.5 mg/L, sulfate 940 mg/L). The contaminants (benzene and toluene), geochemical parameters (sulfate, ORP, and pH), and bacterial community structure in the artificial samples were monitored over time. By the end of this study (day 90), approximately 99% of benzene and 96% of toluene could be eliminated in both S1 and S2 artificial samples, while in the Control artificial sample the contaminant levels remained unchanged due to microbial inactivation. The richness of bacterial communities initially decreased but subsequently increased over time in both S1 and S2 artificial samples. Under sulfate-reducing condition, key players in benzene and toluene degradation were identified as Pseudomonas, Janthinobacterium, Novosphingobium, Staphylococcus, and Bradyrhizobium. The results could provide scientific basis for remediation and risk management strategies at the benzene and toluene contaminated sites.

Influence of the oxidative phosphorylation uncoupler m-chlorophenol on activated sludge production, nutrients removal efficiency and bacterial community structure of a membrane reactor system

In this work, the effects of the metabolic uncoupler meta-chlorophenol (m-CP) on excess sludge production and performance of an MBR system, as well as on activated sludge communities, were investigated. MLVSS were significantly reduced from 8410 mg/L to 5175 mg/L during the first week of the addition of 125 mg/L m-CP, while, thereafter, biosolids were restored to the level prior to uncoupler’s addition. Adding m-CP resulted in more severe effects on nitrifiers rather than organoheterotrophs. Both alkalinity, dissolved oxygen (DO), electrical conductivity (EC) and pH data evidenced the adverse effect of m-CP on the nitrification process. PO43--P concentration drastically raised immediately after m-CP addition from 2.48 ± 0.35 mg/L to 11.84 mg/L, possibly due to the uncoupling of P-release and the hydrolysis of phosphorus reserves. Diversity was highly affected by the addition of m-CP, resulting in the significant decrease of Chao1, Shannon and Fisher indices. By establishing stable operating conditions after m-CP addition, Pseudomonas, Arcanobacterium, Trichococcus, Kocuria and Actinobaculum raised from almost undetectable levels (0.12 % of the total relative abundance) to 35.9 %, 17.8 %, 15.1 %, 11.5 % and 5.7 %, respectively, indicating a massive shift in bacterial community structure, while no nitrifying taxa were detected after m-CP addition.

Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses

Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.

Microbial Community Response to Granular Peroxide-Based Algaecide Treatment of a Cyanobacterial Harmful Algal Bloom in Lake Okeechobee, Florida (USA).

Cyanobacterial harmful algal blooms (cyanoHABs) occur in fresh water globally. These can degrade water quality and produce toxins, resulting in ecological and economic damages. Thus, short-term management methods (i.e., algaecides) are necessary to rapidly mitigate the negative impacts of cyanoHABs. In this study, we assess the efficacy of a hydrogen peroxide-based algaecide (PAK® 27) on a Microcystis dominated bloom which occurred within the Pahokee Marina on Lake Okeechobee, Florida, USA. We observed a significant reduction in chlorophyll a (96.81%), phycocyanin (93.17%), and Microcystis cell counts (99.92%), and a substantial reduction in microcystins (86.7%) 48 h after treatment (HAT). Additionally, there was a significant shift in bacterial community structure 48 HAT, which coincided with an increase in the relative abundance of photosynthetic protists. These results indicate that hydrogen peroxide-based algaecides are an effective treatment method for cyanoHAB control and highlight their effects on non-target microorganisms (i.e., bacteria and protists).

Potential influence of bacterial community structure on the distribution of brGDGTs in surface sediments from Yangtze River Estuary to East China Sea

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are special components of bacterial membrane lipids and are ubiquitously found in diverse terrestrial and marine environments. Acidobacteria have been recently evidenced as one of their source microorganisms in terrigenous environments, such as acidic soils and peats. However, the biological sources of brGDGTs, their distributions and ecophysiological responses, and these biotic impacts on the relationships between brGDGT-based proxies and environmental variables (e.g., ambient temperature, pH, and dissolved oxygen content) in the marine realm are poorly understood. In this study, we analyzed C5- and C6-methylated brGDGTs as well as bacterial communities in the surface sediment samples from the Yangtze River Estuary (YRE) to the East China Sea (ECS), aiming to explore the relationship between brGDGT distribution and bacterial composition and to examine how benthic conditions and bacterial communities jointly influence the spatial patterns of brGDGTs from marine sediments. Substantial differences in the spatial distribution of brGDGTs from coast to shelf were observed. The increase in the proportion of brGDGTs with cyclopentyl and C6-methyl moieties (e.g., Ic and IIc’) and #ringstetra values of >0.7 indicate the occurrence of marine-sourced brGDGTs in the shelf. Statistical analyses suggest that the bacterial community structure and the geochemical and environmental variables may contribute 43.56% and 29.97% to the brGDGT distribution, respectively. Multiple significant correlations between bacterial groups at the order level and brGDGT compounds suggest that bacteria such as Gemmatimonadetes, Planctomycetes and Proteobacteria may potentially contribute to the brGDGT production in marine environments. With the consideration of benthic environmental changes, the shift in bacterial community structure could further result in the variations of brGDGT-based proxies incorporating cyclopentyl and C6-methyl moieties that are likely to be produced by benthic marine bacteria. Overall, in addition to environmental conditions of the ocean bottom, the potential influence of bacterial community structure on the distribution of brGDGTs highlights the caution of using brGDGT-based proxies as terrestrial indicators in coastal oceans.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

ABSTRACT Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

Deciphering the impacts of chromium contamination on soil bacterial communities: A comparative analysis across various soil types

Addressing the widespread concern of chromium (Cr) pollution, this study investigated its impacts on bacterial communities across eight soil types, alongside the potential Cr transformation-related genes. Utilizing real-time PCR, 16S rRNA gene sequencing and gene prediction, we revealed shifts in bacterial community structure and function at three Cr exposure levels. Our results showed that the bacterial abundance in all eight soil types was influenced by Cr to varying extents, with yellow‒brown soil being the most sensitive. The bacterial community composition of different soil types exhibited diverse responses to Cr, with only the relative abundance of Proteobacteria decreasing with increasing Cr concentration across all soil types. Beta diversity analysis revealed that while Cr concentration impacted the assembly process of bacterial communities to a certain extent, the influence on the compositional structure of bacterial communities was primarily driven by soil type rather than Cr concentration. The study also identified biomarkers for each soil type under three Cr levels, offering a basis for monitoring changes in Cr pollution. By predicting crucial functional genes related to Cr transformation, it was observed that the relative abundance of chrA (chromate transporter) in yellow‒brown soil significantly exceeded that in all other soil types, suggesting its potential for Cr adaptation. The study also revealed correlations among soil physicochemical properties, Cr concentration, and these functional genes, providing a foundation for future research aimed at more precise functional analysis and the development of effective soil remediation strategies.

Salinization and sedimentation drive contrasting assembly mechanisms of planktonic and sediment-bound bacterial communities in agricultural streams.

Agriculture is the most dominant land use globally and is projected to increase in the future to support a growing human population but also threatens ecosystem structure and services. Bacteria mediate numerous biogeochemical pathways within ecosystems. Therefore, identifying linkages between stressors associated with agricultural land use and responses of bacterial diversity is an important step in understanding and improving resource management. Here, we use the Mississippi Alluvial Plain (MAP) ecoregion, a highly modified agroecosystem, as a case study to better understand agriculturally associated drivers of stream bacterial diversity and assembly mechanisms. In the MAP, we found that planktonic bacterial communities were strongly influenced by salinity. Tolerant taxa increased with increasing ion concentrations, likely driving homogenous selection which accounted for ~90% of assembly processes. Sediment bacterial phylogenetic diversity increased with increasing agricultural land use and was influenced by sediment particle size, with assembly mechanisms shifting from homogenous to variable selection as differences in median particle size increased. Within individual streams, sediment heterogeneity was correlated with bacterial diversity and a subsidy-stress relationship along the particle size gradient was observed. Planktonic and sediment communities within the same stream also diverged as sediment particle size decreased. Nutrients including carbon, nitrogen, and phosphorus, which tend to be elevated in agroecosystems, were also associated with detectable shifts in bacterial community structure. Collectively, our results establish that two understudied variables, salinity and sediment texture, are the primary drivers of bacterial diversity within the studied agroecosystem, whereas nutrients are secondary drivers. Although numerous macrobiological communities respond negatively, we observed increasing bacterial diversity in response to agricultural stressors including salinization and sedimentation. Elevated taxonomic and phylogenetic bacterial diversity likely increases the probability of detecting community responses to stressors. Thus, bacteria community responses may be more reliable for establishing water quality goals within highly modified agroecosystems that have experienced shifting baselines.

Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan.

To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September). A weighted UniFrac principal coordinate ana-lysis grouped bacterial samples into four clusters along with PC1 (43.8%), corresponding to the four sampling months in the order of sampling dates. Taxonomic ana-lyses revealed that bacterial diversity in the lateral roots was exclusively dominated by three phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) in all samples examined. At the lower taxonomic levels, the dominant taxa were roughly classified into three groups. Therefore, the relative abundances of seven dominant genera (Janthinobacterium, Kribbella, Pedobacter, Rhodanobacter, Sphingobium, Sphingopyxis, and Streptomyces) were the highest in June and gradually decreased as sugar beet grew. The relative abundances of eight taxa (Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Novosphingobium, Phyllobacteriaceae, Pseudomonas, Rhizobiaceae, and Sphingomonas) were mainly high in July and/or August. The relative abundances of six taxa (unclassified Comamonadaceae, Cytophagaceae, unclassified Gammaproteobacteria, Haliangiaceae, unclassified Myxococcales, and Sinobacteraceae) were the highest in September. Among the dominant taxa, 12 genera (Amycolatopsis, Bradyrhizobium, Caulobacter, Devosia, Flavobacterium, Janthinobacterium, Kribbella, Kutzneria, Pedobacter, Rhizobium, Rhodanobacter, and Steroidobacter) were considered to be candidate groups of plant growth-promoting bacteria based on their previously reported beneficial traits as biopesticides and/or biofertilizers.

Contrasting patterns of nitrogen release from fine roots and leaves driven by microbial communities during decomposition

Leachate from decaying root and leaf litter plays crucial roles in soil biogeochemical processes in forest ecosystems. Unlike for leaf litter, however, the chemical composition and microbial community of root litter leachate are poorly understood. We hypothesized that both leachate nitrogen (N) composition and microbial communities differ between plant organs and decomposition stages and that leachate composition affects microbial community composition. We conducted a 2.5-year laboratory incubation using root and leaf substrate from Cryptomeria japonica and Chamaecyparis obtusa. We monitored the N forms released and used metabarcoding to characterize the microbial communities. Leachate N accounted for 40 % and 30 % of net N losses from C. japonica and C. obtusa roots, respectively; the remainder was probably lost in gaseous forms. In contrast, leaves absorbed N during the incubation regardless of tree species. The predominant N form in root leachate was nitrate (NO3−); cumulative NO3− quantity was 22.6 and 25.5 times greater in root than in leaf leachate for C. japonica and C. obtusa, respectively. A nitrifying bacterium was selected as the indicator taxon in root substrates, whereas many families of N-fixing bacteria were selected in leaf substrates. At the end of the incubation period, bacterial taxonomic diversity was high in both organs from both tree species, ranging from 177 to 339 taxa and increasing with time. However, fungal diversity was low for both organs (72 to 155 taxa). Shifts in bacterial community structure were related to NO3− concentration and leachate pH, whereas shifts in fungal community structure were related to leachate pH. These results suggest that the contrasting N dynamics of root and leaf substrates are strongly affected by the characteristics of and the microbes recruited by their leachates. Understanding organ-specific litter N dynamics is indispensable for predicting N cycling for optimal management of forest ecosystems in a changing world.

Pristine and sulfidized zinc oxide nanoparticles alter bacterial communities and metabolite profiles in soybean rhizocompartments

A better understanding of bacterial communities and metabolomic responses to pristine zinc oxide manufacture nanoparticles (ZnO MNPs) and its sulfidized product (s-ZnO MNPs), as well as their corresponding Zn ions in rhizocompartments, critical in the plant-microbe interactions, could contribute to the sustainable development of nano-enabled agriculture. In this study, soybean (Glycine max) were cultivated in soils amended with three Zn forms, namely ZnSO4·7H2O, ZnO MNPs and s-ZnO MNPs at 0, 100 and 500 mg·kg−1 for 70 days. Three Zn forms exposures profoundly decreased the bacterial alpha diversity in roots and nodules. High dose (500 mg·kg−1) groups had a stronger impact on the bacterial beta diversity than low dose (100 mg·kg−1) groups. In the rhizosphere soil and roots, 500 mg·kg−1 of ZnSO4 and s-ZnO MNPs treatments showed the largest shifts in bacterial community structure, respectively. In addition, several significant changed bacterial taxa and metabolites were found at the high dose groups, which were associated with carbon and nitrogen metabolism. PLS-DA plot showed good discrimination in metabolomic profiles of rhizosphere soil and roots between three Zn forms treatments and control. Most metabolic pathways perturbed were closely linked to oxidative stress. Overall, our study indicates either dissolved or nano-particulate Zn exposure at high dose can drastically affected bacterial communities and metabolite profiles in soybean rhizocompartments.

Effects of alder- and salmon-derived nutrients on aquatic bacterial community structure and microbial community metabolism in subarctic lakes.

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r2 = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r2 = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity.

Succession of soil bacterial community along a 46-year choronsequence artificial revegetation in an arid oasis-desert ecotone

How the bacterial community structure and potential metabolic functions will change after revegetation in arid desert ecosystems is still unknown. We used high-throughput pyrosequencing to explore changes in soil bacterial diversity, structure and metabolic pathways, and the key driving factors along a chronosequence of 46-year Haloxylon ammodendron revegetation in an oasis-desert ecotone in the northwestern China. Our results indicated that establishment of H. ammodendron on shifting sand dunes significantly changed the structure of bacterial communities and increased their diversity and richness. The main dominant phyla were Actinobacteria (32.1–41.3%) and Proteobacteria (19.2–27.0%); in that, α-Proteobacteria (16.4–20.7%) were the most abundant Proteobacteria. Kocuria coexisted at different succession stage after year 0, and their relative abundance ranged from 3.8–9.0%. Principal coordinates analysis (PCoA) showed that bacterial community from the same revegetation site grouped together and generally separated from each other, indicating that significant shifts in bacterial community structure occurred after revegetation. LEfSe analysis identified unique biomarkers in the soil samples from seven sites. Moreover, PICRUSt analysis indicated similar overall patterns of metabolic pathways in different succession stage. Redundancy analysis (RDA) showed that total carbon, pH and total phosphorus were major abiotic factors driving the structure of bacterial communities, which explained 57.5% of the variation in bacterial communities. Our findings advance the current understanding of plant-soil interactions in the processes of ecological restoration and desertification reversal.

Co-Treatment with Single and Ternary Mixture Gas of Dimethyl Sulfide, Propanethiol, and Toluene by a Macrokinetic Analysis in a Biotrickling Filter Seeded with Alcaligenes sp. SY1 and Pseudomonas Putida S1

The biotrickling filter (BTF) treatment is an effective way of dealing with air pollution caused by volatile organic compounds (VOCs). However, this approach is typically used for single VOCs treatment but not for the mixtures of VOC and volatile organic sulfur compounds (VOSCs), even if they are often encountered in industrial applications. Therefore, we investigated the performance of BTF for single and ternary mixture gas of dimethyl sulfide (DMS), propanethiol, and toluene, respectively. Results showed that the co-treatment enhanced the removal efficiency of toluene, but not of dimethyl sulfide or propanethiol. Maximum removal rates (rmax) of DMS, propanethiol and toluene were calculated to be 256.41 g·m−3·h−1, 204.08 g·m−3·h−1 and 90.91 g·m−3·h−1, respectively. For a gas mixture of these three constituents, rmax was measured to be 114.94 g·m−3·h−1, 104.17 g·m−3·h−1 and 99.01 g·m−3·h−1, separately. Illumina MiSeq sequencing analysis further indicated that Proteobacteria and Bacteroidetes were the major bacterial groups in BTF packing materials. A shift of bacterial community structure was observed during the biodegradation process.

Gut Microbiota Associated With Different Sea Lamprey (Petromyzon marinus) Life Stages.

Sea lamprey (SL; Petromyzon marinus), one of the oldest living vertebrates, have a complex metamorphic life cycle. Following hatching, SL transition into a microphagous, sediment burrowing larval stage, and after 2–10+ years, the larvae undergo a dramatic metamorphosis, transforming into parasitic juveniles that feed on blood and bodily fluids of fishes; adult lamprey cease feeding, spawn, and die. Since gut microbiota are critical for the overall health of all animals, we examined the microbiota associated with SLs in each life history stage. We show that there were significant differences in the gut bacterial communities associated with the larval, parasitic juvenile, and adult life stages. The transition from larval to the parasitic juvenile stage was marked with a significant shift in bacterial community structure and reduction in alpha diversity. The most abundant SL-associated phyla were Proteobacteria, Fusobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Firmicutes, with their relative abundances varying among the stages. Moreover, while larval SL were enriched with unclassified Fusobacteriaceae, unclassified Verrucomicrobiales and Cetobacterium, members of the genera with fastidious nutritional requirements, such as Streptococcus, Haemophilus, Cutibacterium, Veillonella, and Massilia, were three to four orders of magnitude greater in juveniles than in larvae. In contrast, adult SLs were enriched with Aeromonas, Iodobacter, Shewanella, and Flavobacterium. Collectively, our findings show that bacterial communities in the SL gut are dramatically different among its life stages. Understanding how these communities change over time within and among SL life stages may shed more light on the role that these gut microbes play in host growth and fitness.

Resistance of microbial community and its functional sensitivity in the rhizosphere hotspots to drought

Climate change impacts soil microbial communities, activities and functionality. Nonetheless, responses of the microbiome in soil microenvironments with contrasting substrate availability in the rhizosphere to climatic stresses such as drought are largely unknown. To fill this knowledge gap, we coupled soil zymography with site-specific micro-sampling of the soil and subsequent high-throughput sequencing. This helped identify how the bacterial community structure and the genes encoding N-cycling enzymes (leucine aminopeptidase and chitinase) in rhizosphere hotspots and coldspots (microsites with activities in the range of bulk soil but localized within the rhizosphere) of maize respond to drought (20% WHC, two weeks).The elevated activities of leucine aminopeptidase and chitinase in rhizosphere hotspots were caused by the tight collaborative relationships between bacteria and their stable network structure rather than by any significant shift in bacterial community structure or enzyme-encoding gene copies. Despite the similarity in bacterial community structure in soil under drought and optimal moisture, functional predictions indicated the increased relative abundance of genera belonging to Actinobacteria capable of leucine aminopeptidase and chitinase production, especially Streptomyces, Nocardioides, Marmoricola, and Knoellia. Accordingly, the number of gene copies encoded by Actinobacteria for these two enzymes increased by 5.0–17% under drought. Among the bacteria with increased relative abundance under drought, Luedemannella played a crucial role in mediating nutrients and energy fluxes between bacteria. This was reflected in a 35–70% increase in leucine aminopeptidase and chitinase activities under drought. The resistance of enzyme activities to drought was higher in hotpots than that in coldspots. These results revealed that rhizosphere bacterial community composition remained stable, and that the number of gene copies encoded by Actinobacteria responsible for N-cycling enzymes increased under drought. The expected reduction of processes of N cycle was absent. Instead, bacteria increased N mining rate in those hotspots remaining active despite water scarcity.

Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils

Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.

Wastewater effluents cause microbial community shifts and change trophic status

Widespread wastewater pollution is one of the greatest challenges threatening the sustainable management of rivers globally. Understanding microbial responses to gradients in environmental stressors, such as wastewater pollution, is crucial to identify thresholds of community change and to develop management strategies that protect ecosystem integrity. This study used multiple lines of empirical evidence, including a novel combination of microbial ecotoxicology methods in the laboratory and field to link pressure-stressor-response relationships. Specifically, community-based whole effluent toxicity (WET) testing and environmental genomics were integrated to determine real-world community interactions, shifts and functional change in response to wastewater pollution. Here we show that wastewater effluents above moderate (>10%) concentrations caused consistent significant shifts in bacterial community structure and function. These thresholds of community shifts were also linked to changes in the trophic state of receiving waters in terms of nutrient concentrations. Differences in the community responses along the effluent concentration gradient were primarily driven by two globally relevant bacterial indicator taxa, namely Malikia spp. (Burkholderiales) and hgcI_clade (Frankiales). Species replacement occurred above moderate effluent concentrations with abundances of Malikia spp. increasing, while abundances of hgcI_clade decreased. The responses of Malikia spp. and hgcI_clade matched gene patterns associated with globally important nitrogen cycling pathways, such as denitrification and nitrogen fixation, which linked the core individual taxa to putative function and ecosystem processes, rarely achieved in previous studies. This study has identified potential indicators of change in trophic status and the functional consequences of wastewater pollution. These findings have immediate implications for both the management of environmental stressors and protection of aquatic ecosystems.

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem.

Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.