Functional Gene Diversity Research Articles

Effect of red kaolin on the diversity of functional genes based on Kyoto Encyclopedia of Genes and Genomes pathways during chicken manure composting

The transcription and expression of functional genes governed the biotransformation of nutrients during composting. In this study, the diversities of functional genes were investigated in 50 days chicken manure composting through six treatments amended with different dosage of red kaolin. Results showed that based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Metabolism possessed largest proportion and richest genes number among six pathways, of which carbohydrate metabolism (81007) were significantly greater than others; while Human Disease and Organismal Systems were relatively lower. Meanwhile, the addition of red kaolin has an important impact on dynamics of KEGG genes, the relative abundance of detected genes were distinctively different in all treatments. Similarity analysis also showed the varying influence of different proportion of red kaolin on functional genes during chicken manure composting. In conclusion, application of red kaolin in chicken manure composting effectively improved the relative abundance of functional genes.

An assessment of the functional enzymes and corresponding genes in chicken manure and wheat straw composted with addition of clay via meta-genomic analysis

The transcription and expression of functional genes and metabolic function of enzymes governed the transformation of nutrients during composting process. The diversities of functional enzymes and corresponding genes were investigated in 50 days chicken manure composting through six treatments amended with six different dosage of clay in this study. The result revealed that the relative abundance of functional enzymes and related genes was distinctively different among all treatments. The addition of clay significantly enhanced the diversity of functional genes and enzymes at different levels in this study, similarity analysis also showed the different proportion of clay addition influence activity of functional genes and enzymes in varying degrees. The higher percentage of clay addition showed more significant promotion on dynamics of functional genes and enzymes. While, at six major functional level, the gene expression and related enzymatic activity was inhibited with addition of 10% clay. In conclusion, application of clay in chicken manure composting could effectively improve the relative abundance of functional genes and enzymes, so as to promote degradation of organic matter during composting.

High starter phosphorus fertilization facilitates soil phosphorus turnover by promoting microbial functional interaction in an arable soil

Microbial phosphorus (P) turnover is critical in C utilization efficiency in agroecosystems. It is therefore necessary to understand the P mobilization processes occurring during P fertilization in order to ensure both crop yield and environmental quality. Here, we established a controlled pot experiment containing soil amended with three different levels of starter P fertilizer and collected soil samples after 30, 60, and 90 days of incubation. Quantitative microbial element cycling (QMEC) smart chip technology and 16S rRNA gene sequencing were used to investigate functional gene structures involved in carbon, nitrogen and P cycling and the bacterial community composition of the collected samples. Although P fertilization did not significantly affect the structure of the soil microbial community, some rare microbiota were changed in particular phosphorus-solubilizing bacteria were enriched at the high P fertilization level, suggesting that the rare taxa make an important contribution to P turnover. P fertilization also altered the functional gene structure, and high P concentrations enhanced the functional gene diversity and abundance. Partial redundancy analysis further revealed that changes in rare taxa and functional genes of soil microorganisms drive the alteration of soil P pools. These findings extend our understanding of the microbial mechanisms of P turnover.

Microbial functional gene diversity in natural secondary forest Ultisols

The diversity and biogeography of functional genes at a regional scale remains unclear. We hypothesize that plant community composition, nutrient availability, and spatial distance are driving factors for the functional gene diversity of soil microorganisms at a regional scale. We also hypothesize that different functional genes have different responses to environment. Using functional gene arrays (GeoChip 3.0), we examined microbial diversity, and influencing factors in Ultisols in 11 natural secondary forest plots in southern China which contained 4073 functional genes averagely. Carbon and nitrogen cycle genes were more variable than genes involved in phosphorus utilization, organic remediation, and metal resistance, in similar trends with soil substrate availability. Genes involved in nitrification being more variable than other nitrogen cycling genes; phytase genes being more variable than polyphosphate kinase genes (ppk) and exopolyphosphatase genes (ppx); exoglucanase and endoglucanase genes being more variable than cellobiase genes; lignin peroxidase genes (lip) being more variable than manganese peroxidase genes (mnp). Approximately 41% of the variation in gene composition could be explained by fine root surface area, available nitrogen, and the largest spatial scale factor, with the former two environmental factors over influenced spatial distance. Both environmental factors (represented by nutrient availability) and spatial distance influenced microbial functional gene composition, while the influence of spatial distance worked through environmental factors in natural secondary forest in Ultisols within approximately 500 km, providing insights into microbial biogeography from a functional gene perspective.

Application of biogas slurry rather than biochar increases soil microbial functional gene signal intensity and diversity in a poplar plantation

Microbes play critical roles in the cycling of nutrients in forest ecosystems. Many studies have shown that the application of organic fertilizer can alter bacterial diversity; however, the responses of soil microbial functional genes to organic fertilization (particularly biogas slurry fertilization, or in combination with biochar) have not been elucidated as yet. We examined the responses of the abundance, diversity, and composition of soil microbial functional genes under five-years of fertilization. This fertilization involved low and high application rates of biogas slurry, at 250 and 375 m3 ha−1 yr−1, respectively, or in combination with low and high application rates of biochar, at 80 and 120 t ha−1, respectively, in a coastal poplar plantation of Eastern China. Compared to the control, the normalized signal intensity of genes in the major functional categories increased significantly in response to the quantity of applied biogas slurry, but insignificantly in response to the additional application of biochar. Subsequent to the application of biogas slurry, the functional gene evenness and Shannon index increased significantly; however, the addition of biochar to the biogas slurry had insignificant effects on the α-diversity of functional genes. These functional gene compositions under five different treatments were well distinguished, primarily through the application of biogas slurry. Our results revealed that the abundance of a large number of key functional genes involved in C, N, and P cycling were effectively increased, and these changes were well correlated with most soil properties. This study reveals the molecular level mechanisms that promote plant growth following organic fertilizer application, through the enhancement of soil microbial functional gene diversity.

Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem

Riparian buffer systems (RBS) are considered a best management practice (BMP) in agricultural landscapes to intercept soil nitrogen (N) and phosphorus (P) leaching and surface runoff into aquatic ecosystems. However, these environmental benefits could be offset by increased greenhouse gas (GHG) emissions, including nitrous oxide (N2O). The main sources of N2O in soil are linked to processes which are mediated by soil microbial communities. These microorganisms play crucial roles in N-cycling and in the reduction of nitrate to N2, and N2O gases. This study was conducted to determine the abundance and diversity of microbial communities and functional genes associated with N-cycling and their influence on N2O emissions in different riparian land-use: undisturbed natural forest (UNF), rehabilitated site (RH), grass buffer (GRB), and an adjacent agricultural land (AGR). Soil was sampled concurrently with N2O emissions on July 13, 2017. DNA was extracted and used to target key N-cycling genes for N-fixation (nifH), nitrification: (amoA), and denitrification (nirS, nirK, and nosZ) via quantitative PCR, and for high throughput sequencing of total bacterial and fungal communities. Non-metric multidimensional scaling (NMDS) was used to examine microbial community composition and indicated significant differences in bacterial (p < 0.001) and fungal (p < 0.0085) communities between sites. Bacterial abundance differed significantly (p = 0.0005) between RBS and AGR sites with the highest populations occurring in the UNF (2.1 × 1010 copies g−1 dry soil), and lowest in AGR (5.3 × 109 copies g−1 dry soil). However, the AGR site had the highest ammonia-oxidizing bacteria (AOB) abundance, indicating that nitrification is highest at this site. The abundance of the nosZ gene was highest in RH and GRB demonstrating the capacity for complete denitrification at these sites, lowering measured N2O. These results suggest N-cycling microbial community dynamics differ among RBS and are influencing N2O emissions in the sites investigated.

Functional diversity and abundance of nitrogen cycle-related genes in paddy soil

The nitrogen cycle and the associated microbes play an important role in natural ecosystems, including terrestrial habitats; they also have a major effect on climate change. The aim of this study was to explore microbial communities in rice paddy soil by detecting and quantifying some key functional genes involved in the nitrogen cycle using molecular techniques such as conventional polymerase chain reaction (PCR), clone library construction, sequencing, phylogenetic analysis, and real-time PCR. The genes analyzed were as follows: nitrogenase reductase gene (nifH), hydrazine synthase gene (hzsA), nitrous oxide reductase gene (nosZ), copper-containing (nirK) and cytochrome cd1-containing (nirS) nitrite reductase genes, nitrite oxidoreductase gene (nxrB), and ammonium monooxygenase gene (amoA). The sequence assessment using the clone library targeting these genes revealed high diversity and dominance of bacterial communities. Furthermore, real-time PCR using SYBR green dye and some primers specific for each gene revealed the high abundance of nxrB (4.1 × 109 ± 0.4 × 109 copies g−1 soil) and low abundance of hzsA (4.0 × 105 ± 1.1 × 105 copies g−1 soil). The findings of our study will be useful to explore microbial communities in terrestrial habitats, such as agricultural paddy fields.

Partial function prediction of sulfate-reducing bacterial community from the rhizospheres of two typical coastal wetland plants in China

Sulfate-reducing bacteria (SRB) are ubiquitous anaerobic microorganisms that play significant roles in the global biogeochemical cycle. Coastal wetlands, one of the major habitats of SRB, exhibit high sulfate-reducing activity and thus play significant roles in organic carbon remineralization, benthic geochemical action, and plant-microbe interactions. Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors. Therefore, in this study, functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China: Zostera japonica and Scirpus mariqueter. To this end, some physicochemical characteristics of the sediments as well as the phylogenetic structure, community composition, diversity, and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed. The Z. japonica meadow had a higher dissimilatory sulfate reduction capability than the S. mariqueter-comprising saltmarsh, owing to its larger proportion of SRB in the microbial community, larger proportions of functional genes involved in dissimilatory sulfate reduction, and the stronger ability of the SRB to degrade organic substrates completely. This study confirmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB, which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.

Effects of atrazine on the black community land function and role of microbial ecology

By measuring the concentration of atrazine stress and different culture days, the abundance of key genes in soil nitrogen transformation was studied by means of real-time PCR with the increase of atrazine stress time. The abundance of soil nitrogen-fixing function gene (nif-H) increased significantly with the increase of time in the middle and late culture period (15-30 d), indicating that the abundance of soil nitrogen-fixing function gene was promoted; soil ammonia oxidation. The abundance of functional gene (amo A) was reduced at the low concentration of atrazine (0 mg/kg, 20 mg/kg), and then decreased with increasing stress time, while at high concentration of atrazine. Under the treatment of (100mg/kg), with the increase of time, the abundance of soil ammonia oxidation function increased first and then decreased, indicating that the abundance of soil ammonia oxidation function gene was affected in the process of culture. II Based on high-throughput sequencing technology, the results of soil nitrogen fixation and ammonia oxidation community diversity showed that the functional gene diversity of soil samples was affected by the concentration of atrazine and stress time. According to the analysis of soil diversity index, nitrogen-fixing functional genes of soil samples treated with atrazine at 0 mg/kg, 20 mg/kg and 100 mg/kg were tested at the late stage (30 d). The diversity index of (nif-H) was higher than the mid-test (15 d). At the beginning of the experiment (0 d), the ammonia functional gene (amo A) diversity index of soil samples treated with atrazine concentrations of 0 mg/kg, 20 mg/kg and 100 mg/kg was higher than that in the middle of the experiment (15d), studies have shown that the nitrogen and ammonia oxidation functional gene diversity is affected under different concentrations of atrazine stress time. The distribution of the nitrogen-fixing gene (nif-H) and the ammonia-oxidizing functional gene (amo A) in the horizontal sample community structure showed that the nitrogen-fixing gene was in the middle of culture (15 d), and the genus Burkholderia and Rhizobium were earlier than the culture period (0d) indicating that the above two types of nitrogen-fixing microorganisms play a leading role at this stage. Throughout the experiment (0-30 d), the number of nitrogen-fixing functional genes in the blank treatment was higher than 20 mg/kg and 200 mg/kg. The principal component analysis confirmed that the different culture days and different stress concentrations of atrazine had certain effects on the composition of soil nif-H and amo A gene communities.

Genome-Wide Identification of Aluminum-Activated Malate Transporter (ALMT) Gene Family in Rubber Trees (Hevea brasiliensis) Highlights Their Involvement in Aluminum Detoxification

The rubber tree (Hevea brasiliensis) is a widely cultivated crop in tropical acidic soil that is tolerant to high concentration of aluminum and the aluminum-activated malate transporter (ALMT) plays an important role in plant aluminum detoxification. However, the effects of ALMT on rubber tree aluminum tolerance, growth performance, and latex production are unclear. In this study, 17 HbALMT genes were identified from the genome of rubber trees. The physiological and biochemical characteristics, phylogenetic relationships, gene structures, conserved motifs, cis-elements of promoter, and expression patterns of the identified HbALMT genes were studied. Phylogenetic relationships indicated that these genes were divided into four clusters and genes in the same cluster have similar gene structures and conserved motifs. The promoters of HbALMT genes contain many cis-elements associated with biotic stress and abiotic stress. Quantitative real-time PCR analysis revealed HbALMTs showed various expression patterns in different tissues, indicating the functional diversity of HbALMT genes in different tissues of rubber trees. Transcriptome analysis and qRT-PCR assay showed that most of the HbALMT genes responded to aluminum stress, and among the 17 HbALMTs, HbALMT1, HbALMT2, HbALMT13, and HbALMT15 displayed higher expression levels in roots after two or five days of Al treatments, indicating their potential involvement in aluminum detoxification. Taken together, this study laid a foundation for further understanding the molecular evolution of the ALMT genes and their involvement in rubber tree aluminum adaption.

Carbon nanomaterials affect carbon cycle-related functions of the soil microbial community and the coupling of nutrient cycles

Many studies have examined changes in soil microbial community structure and composition by carbon nanomaterials (CNMs). Few, however, have investigated their impact on microbial community functions. This study explored how fullerene (C60) and multi-walled carbon nanotubes (M50) altered functionality of an agricultural soil microbial community (Archaea, Bacteria and Eukarya), using microcosm experiments combined with GeoChip microarray. M50 had a stronger effect than C60 on alpha diversity of microbial functional genes; both CNMs increased beta diversity, resulting in functional profiles distinct from the control. M50 exerted a broader, severer impact on microbially mediated nutrient cycles. Together, these two CNMs affected CO2 fixation pathways, microbial degradation of diverse carbohydrates, secondary plant metabolites, lipids and phospholipids, proteins, as well as methanogenesis and methane oxidation. They also suppressed nitrogen fixation, nitrification, dissimilatory nitrogen reduction, eukaryotic assimilatory nitrogen reduction, and anaerobic ammonium oxidation (anammox). Phosphorus and sulfur cycles were less vulnerable; only phytic acid hydrolysis and sulfite reduction were inhibited by M50 but not C60. Network analysis suggested decoupling of nutrient cycles by CNMs, manifesting closer and more hierarchical gene networks. This work reinforces profound impact of CNMs on soil microbial community functions and ecosystem services, laying a path for future investigation in this direction.

Optimization of key factors affecting hydrogen production from coffee waste using factorial design and metagenomic analysis of the microbial community

The objective of this study was to evaluate the fermentation conditions that led to the optimization of H2 production from coffee waste (wastewater, pulp and husk) and the taxonomic and functional characterization of autochthonous microorganisms. Assays in batch reactors with microbial consortium bioaugmentation (bacteria and fungi) evaluated the pH (4.82–8.18), pulp and husk concentration (6.95–17.05 g/L) and headspace factor (33.18–66.82%) by means of rotational central composite design and response surface. Operating conditions in the reactor optimized for 3.04 LH2/Ld were at pH 7.0, 7 g/L pulp and husk and 30% headspace. The main metabolites observed were butyric acid (3838 mg/L), isobutyric acid (506 mg/L), methanol (226 mg/L) and butanol (156 mg/L). Clostridium sp. (87.9%), Lactobacillus sp. (1.7%), Kazachstania sp. (18.6%) and Saccharomyces sp. (16.3%) were the main genera identified in the optimized reactor, which had functional gene diversity for H2 production, alcoholic fermentation, cellulose degradation, lignin, hemicellulose and phenol.

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds.

Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.

Distinct drivers of functional diversity.

This study observed that the functional diversity of core and accessory genes in the soil microbiome are governed by distinct processes.

Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca).

Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from “endangered” to “vulnerable” (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild.

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes.

It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.

MountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.

Alternative transcription start (ATS) and alternative polyadenylation (APA) create alternative RNA isoforms and modulate many aspects of RNA expression and protein production. However, ATS and APA remain difficult to detect in RNA sequencing (RNA-seq). Here, we developed mountainClimber, a de novo cumulative-sum-based approach to identify ATS and APA as change points. Unlike many existing methods, mountainClimber runs on a single sample and identifies multiple ATS or APA sites anywhere in the transcript. We analyzed 2,342 GTEx samples (36 tissues, 215 individuals) and found that tissue type is the predominant driver of transcript end variations. 75% and 65% of genes exhibited differential APA and ATS across tissues, respectively. In particular, testis displayed longer 5' untranslated regions (UTRs) and shorter 3' UTRs, often in genes related to testis-specific biology. Overall, we report the largest study of transcript ends across human tissues to our knowledge. mountainClimber is available at github.com/gxiaolab/mountainClimber.

High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer

Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average > 50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.

Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents.

Evergreen broad‐leaved (EBF) and deciduous broad‐leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad‐leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = −0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad‐leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.

High bacterial diversity in nearshore and oceanic biofilms and their influence on larval settlement by Hydroides elegans (Polychaeta).

Settlement of many benthic marine invertebrates is stimulated by bacterial biofilms, although it is not known if patterns of settlement reflect microbial communities that are specific to discrete habitats. Here, we characterized the taxonomic and functional gene diversity (16S rRNA gene amplicon and metagenomic sequencing analyses), as well as the specific bacterial abundances, in biofilms from diverse nearby and distant locations, both inshore and offshore, and tested them for their ability to induce settlement of the biofouling tubeworm Hydroides elegans, an inhabitant of bays and harbours around the world. We found that compositions of the bacterial biofilms were site specific, with the greatest differences between inshore and offshore sites. Further, biofilms were highly diverse in their taxonomic and functional compositions across inshore sites, while relatively low diversity was found at offshore sites. Hydroides elegans settled on all biofilms tested, with settlement strongly correlated with bacterial abundance. Bacterial density in biofilms was positively correlated with biofilm age. Our results suggest that the localized distribution of H. elegans is not determined by 'selection' to locations by specific bacteria, but it is more likely linked to the prevailing local ecology and oceanographic features that affect the development of dense biofilms and the occurrence of larvae.