Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica

Effects of Fe-N co-modified biochar on methanogenesis performance, microbial community, and metabolic pathway during anaerobic co-digestion of alternanthera philoxeroides and cow manure

The performance of anaerobic digestion (AD) is susceptible to disturbances in feedstock degradation, intermediates accumulation, and methanogenic archaea activity. To improve the methanogenesis performance of the AD system, Fe-N co-modified biochar was prepared under different pyrolysis temperatures (300,500, and 700 °C). Meanwhile, pristine and Fe-modified biochar were also derived from alternanthera philoxeroides (AP). The aim was to compare the effects of Fe-N co-modification, Fe modification, and pristine biochar on the methanogenic performance and explicit the responding mechanism of the microbial community in anaerobic co-digestion (coAD) of AP and cow manure (CM). The highest cumulative methane production was obtained with the addition of Fe-N-BC500 (260.38 mL/gVS), which was 42.37 % higher than the control, while the acetic acid, propionic acid, and butyric acid concentration of Fe-N-BC were increased by 147.58 %, 44.25 %, and 194.06 % compared with the control, respectively. The co-modified biochar enhanced the abundance of Chloroflexi and Methanosarcina in the AD system. Metabolic pathway analysis revealed that the increased methane production was related to the formation and metabolism of volatile fatty acids and that Fe-N-BC500 enhanced the biosynthesis of coenzyme A and the cell activity of microorganisms, accelerating the degradation of propionic acid and enhancing the hydrogenotrophic methanogenesis pathway. Overall, Fe-N co-modified biochar was proved to be an effective promoter for accelerated methane production during AD.

Effects of water environmental factors and antibiotics on bacterial community in urban landscape lakes

The presence of antibiotics can affect the natural microbial community and exert selective pressure on the environment's microorganisms. This study focused on three types of urban landscape lakes in Xi'an that were closely related to human activities. By combining basic water quality indicators, antibiotic occurrence status, bacterial communities and their potential metabolic functions, Spearman correlation coefficient and redundancy analysis were used to explore the relationship between them, and further explore the impact mechanism of environmental factors and antibiotics on bacterial community structure. The results showed that ofloxacin, erythromycin, and roxithromycin were the main types of antibiotics in the three landscape lakes, with low ecological risks, and there was a clear clustering of antibiotic occurrence. Proteobacteria was the most abundant bacterial phylum, and each lake had its own unique dominant bacteria, which indicates that they are influenced by varying water sources, pollution, and other nearby environments. Statistical analysis showed that pH and nitrogen nutrients were the most critical environmental factors affecting bacterial communities (P<0.01), while tetracyclines and lincomycins were the antibiotics that had a significant impact on bacterial communities (P<0.05). Antibiotics mainly promote defense- and signal transduction-related functions, and inhibit the metabolic activity of bacterial communities. However, the impact of antibiotics on bacterial diversity, community structure, and potential metabolic function in the three urban lakes was less than that of environmental factors. These results help to clarify the mechanism and degree of impact of different interference factors (environmental factors, conventional pollutants, and antibiotics) on bacterial communities in the water environment and are important for the management of urban landscape lake water environments.

Spatio-temporal dynamics of phytoplankton in a diversion reservoir and the major influencing factors: taxonomic versus functional groups classification

Identifying factors affecting phytoplankton dynamics is crucial to the management of aquatic ecosystems. A lot of scholars have conducted intensive studies on phytoplankton in lake or reservoirs, but not many studies have been conducted on diversion reservoirs. To explore the seasonal and spatial variation of phytoplankton communities and their relationship with environmental factors in the context of water diversion, a case study was carried out at XiKeng (XK) reservoir in South China. In this study, month-by-month water samples and phytoplankton were collected from this reservoir from December, 2021, to July, 2022. The results showed that the phytoplankton community was characterized by significant spatial and temporal variations. There were significant differences in phytoplankton abundance and structure in the reservoirs in terms of time. The abundance of phytoplankton cells and the proportion of Cyanobacteria in the reservoir showed a trend of increasing from autumn to spring and then decreasing from spring to summer, while the functional group evolved from S1 in autumn to SN in spring and summer. The abundance of phytoplankton was influenced by the dynamic water division and the characteristics of the reservoir itself, resulting in a spatial distribution characteristic of AIII > AII > AI. Water temperature (WT) and nutrients were the key factors driving the changes in phytoplankton abundance and community structure in the reservoir. These findings will deepen our understanding of the spatial and temporal dynamics of phytoplankton community structure in diversion reservoirs and provide a basis for freshwater water ecological management strategies.

Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes

Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.

Characterization of Changes in Penile Microbiome Following Pediatric Circumcision

BACKGROUND

While microbiome and host regulation contribute independently to many disease states, it is unclear how circumcision in pediatric population influences subsequent changes in penile microbiome.

OBJECTIVE

Our study aims to analyze jointly paired taxonomic profiles and assess pathways implicated in inflammation, barrier protection, and energy metabolism.

DESIGN, SETTING, AND PARTICIPANTS

We analyzed 11 paired samples, periurethral collection, before and after circumcision, to generate microbiome and mycobiome profiling. Sample preparation of 16S ribosomal RNA and internal transcribed spacer sequencing was adapted from the methods developed by the National Institutes of Health Human Microbiome Project.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We obtained the predictive functional attributes of the microbial communities between samples using Silva-Tax4Fun and the Greengenes-Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) approach. The predictive functioning of the microbial communities was determined by linearly combining the normalized taxonomic abundances into the precomputed association matrix of Kyoto Encyclopedia of Genes and Genomes orthology reference profiles.

RESULTS AND LIMITATIONS

Several notable microbiome and mycobiome compositional differences were observed between pre- and postcircumcision patients. Pairwise comparisons across taxa revealed a significant decrease (p < 0.05, false discovery rate corrected) of microbiome organisms (Clostridiales, Bacteroidales, and Campylobacterales) and mycobiome (Saccharomycetales and Pleosporales) following circumcision. A total of 14 pathways were found to differ in abundance between the pre- and postcircumcision groups (p < 0.005, false discovery rate <0.1 and linear discriminant analysis score >3; five enriched and nine depleted). The pathways reduced after circumcision were mostly involved with amino acid and glucose metabolism, while pathways prior to circumcision were enriched in genetic information processing and transcription processes. As expected, enrichment in methyl-accepting chemotaxis protein, an integral membrane protein involved in directed motility of microbes to chemical cues and environment, occurred prior to circumcision, while the filamentous hemagglutinin pathway (a strong immunogenic protein) was depleted after circumcision CONCLUSIONS: Our results offer greater insight into the host-microbiota relationship of penile circumcision and may serve to lay the groundwork for future studies focused on drivers of inflammation, infection, and oncogenesis.

PATIENT SUMMARY

Our study showed a significant reduction in bacteria and fungi after circumcision, particularly anaerobic bacteria, which are known to be potential inducers of inflammation and cancer. This is the first study of its kind showing the changes in microbiome after circumcision, and some of the changes that occur in healthy infants after circumcision that may explain the differences in cancer and inflammatory disorders in adulthood.

A multifaceted screening of applied voltages for electro-assisted anaerobic digestion of blackwater: Significance of temperature, hydrolysis/acidogenesis, electrode corrosion, and energy efficiencies

A microbial electrolysis cell-assisted anaerobic digester (MEC-AD) was operated with vacuum toilet blackwater at different applied voltages (0-1.6 V) at room temperature (R₂₀). A parallel MEC-AD was operated at 35 °C (R₃₅) to provide a kinetics index at mesophilic temperature. Both reactors failed at 1.6 V due to the alkaline pH created by anodic corrosion. In R₂₀, the best performance was observed at 1.2 V, with methane yield, COD removal, hydrolysis and acidogenesis efficiency increased by 59.9%, 27.0%, 52.0%, and 44.9%, respectively, compared to those of 0 V. Enrichment of hydrolytic and syntrophic bacteria (e.g., Clostridium, Bacteroidales, Sedimentibacter, Syntrophomonas) and increased abundance of genes encoding complex organics (e.g., proteins, carbohydrates, lipids) metabolism in R₂₀ at 1.2 V corresponded to the enhanced hydrolysis/acidogenesis processes. R₂₀ at 1.2 V generated 1.16 times more net energy than R₃₅ at the optimum voltage for methane yield (0.8 V), indicating ambient temperature operation of MEC-AD systems would be a more sustainable strategy.

Zeolite mediated processing of nitrogenous waste in the rearing environment influences gut and sediment microbial community in freshwater crayfish (Cherax cainii) culture

Zeolite is known to uptake toxic metals and filter nitrogenous waste from aquaculture effluents. The present study aimed to investigate the impacts of zeolite in three different applications namely, dietary zeolite (DZ), suspended zeolite (SZ) in the water column, and a combination of both (DZSZ) relative to unexposed freshwater crayfish, marron (control). At the end of the 56-days trial, the impact was assessed in terms of characterization of microbial communities in the culture environment and the intestine of marron. Alongside the microbial communities, the innate immune response of marron was also evaluated. The 16S rRNA data showed that marrons exposed to the suspended zeolite had a significant increase of bacterial diversity in the gut, including the restoration of marron core operational taxonomic units (OTUs), relative to other forms of exposures (DZ, DZSZ) and the control. Suspended zeolite alone also increased the number of unshared OTUs and genera, and improved predicted metabolic functions for the biosynthesis and digestion of proteins, amino acids, fatty acids, and hormones. In the tank sediment, the shift of microbial communities was connected more strongly with the time of experiment than the type of zeolite exposure. In the second case, only control marron had a different microbial ordination in terms of rare taxa present in the community. Nevertheless, the modulation in the gut environment was found more prominent in DZ, relative to modulation in the tank sediments. The taxa-environment correlation identified Rhodoferax as the most potential bacteria in removing nitrogenous waste from the rearing environment. Further analysis showed that SZ resulted in the upregulation of genes associated with the innate immune response of marron. Overall results suggest that SZ can be used to enrich microbial communities in the gut and tank sediments and better immune performance of marron.

Microbial ecology of biofiltration used for producing safe drinking water

Abstract

Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application.

Key points

• Biofilters are composed of complex microbiomes, primarily shaped by water quality.

• Conventional biofilters contribute to address safety challenges in drinking water.

• Studies may underestimate the active/functional role of microbiomes in biofilters.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12013-x.

Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season

Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake’s water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH₄⁺, and NO₃^–. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.

Inferring microbiota functions from taxonomic genes: a review

Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.

Hepato and nephroprotective activity of methanol extract of Hygrophila spinosa and its antibacterial potential against multidrug resistant Pandoraea sputorum

This research was aimed to evaluate the phytochemical profile, bactericidal activity of Hygrophila spinosa against multidrug resistant Pandoraea sputorum and assess their antioxidant competence against various radicals and studied their hepatoprotective and nephroprotective activity on HepG2 and HEK 293 cell line. The results showed that the methanol extract has various phytochemical components with reasonable quantity. Fortunately, the multidrug-resistant P. sputorum was sensitive (22.8 ± 0.2 mm of the zone of inhibition) at 15 mg mL^-1 concentration of methanol extract. The higher concentration of phenolic and other phytochemical components, showed significant antioxidant activity against ferric, DPPH, hydroxyl, and ABTS radicals, with IC₅₀ values of 71.09, 64.333, 91.157, and 104.931 g mL^-1, respectively. Surprisingly, the methanol extract possesses hepato and nephroprotective activity against CCl₄ and cisplatin-induced cytotoxicity on HepG2 and HEK 293 cell lines, respectively. It maintains the cell viability as up to 90.48% and 90.35% of HepG2 and EK 293 cell line at the concentration of 20 μg mL^-1. The FTIR analysis states that the methanol extract possesses a significant functional group responsible for these multi-potential activities. These results suggest that, the methanol extract of H. spinosa might contain the most significant bioactive components with outstanding medicinal properties.

Effects of different antimony contamination levels on paddy soil bacterial diversity and community structure

To clarify the response mechanism of paddy soil microorganisms to contamination caused by antimony (Sb) alone, we added K(SbO)C₄H₄O₆.1/2 H₂O with different contents to uncontaminated paddy soil and carried out related studies. 16S rRNA was sequenced in V3-V4 regions of paddy soil bacteria with different Sb contamination levels. Then, α diversity and species enrichment and separation of paddy soil microorganisms were analyzed. The biochemical behavior and the influences of Sb fractions on bacterial communities and ecological function were explored in paddy soil with different contamination levels. The results showed that the contents of Sb_tot and Sb(V) increased with the increase of contamination level, and the difference was significant among the groups. For Sb_exe and Sb_srp there were slight differences between S100 and S200 groups, but significant differences among other groups. The diversity index increased with the increase of Sb concentration, which reached the maximum value in S200 group and the minimum value in control group (SC). The relative importance analysis demonstrated that Sb(III) and Sb_srp were the main Sb fractions affecting the diversity index of bacterial community. In addition, the results of principal coordinate analysis (PCoA) showed that there were significant differences between the bacterial communities in SC and in the soil with different Sb contamination levels. Based on diversity analysis, it was found that Proteobacteria, Actinobacteria and Bacteroidetes were the main dominant phyla in paddy soil with different Sb concentrations, and their enrichment and separation were greater than those of other dominant phyla. Though the Static Bayesian network inference, it was shown that Sb_tot affected Sphingomonadaceae, and Sb_srp affected Burkholderiaceae, Xanthomonadaceae and Acidobacteriale to further affect bacterial communities, while Sb(V) mainly affected Flavobacteriaceae, Rhodopirillaceae and Acidobacteriale. The above results provide a scientific basis for the biochemical restoration potential of paddy soils with different Sb contamination levels.

Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms

Applying low concentrations of hydrogen peroxide (H₂O₂) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H₂O₂, little is known about the impacts of these H₂O₂ treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H₂O₂ concentrations (target: 2.5 mg L⁻¹) and in two series of controlled lake incubations. The results show that the H₂O₂ treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H₂O₂ addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H₂O₂ to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage

The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.

Bacterial diversity and predicted enzymatic function in a multipurpose surface water system - from wastewater effluent discharges to drinking water production

BACKGROUND

Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics -from the source of contamination, through the watershed to the DW production process-may help safeguard human health and the environment.

RESULTS

The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemäenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p <  0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 ± 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 ± 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66-80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (≥13%) than in other groups (≤3%). Acidobacteria was more abundant in the DW treatment process (≥13%) than in others (≤2%). In total, the share of PHRB reads was higher in sewage and surface water than in the DW treatment samples. The seasonal effect in bacterial communities was observed only on surface water samples, with the lowest diversity during summer.

CONCLUSIONS

The low bacterial diversity and absence of PHRB read in the DW samples indicate AGR can produce biologically stable and microbiologically safe drinking water. Furthermore, the significantly different bacterial communities at the pollution sources compared to surface water and DW samples highlight the importance of effective wastewater treatment for protecting the environment and human health.

Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades?

We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e., a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in previous studies on the microbial community of tardigrades, and Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.

Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes

Gut microbiota have important roles in the survival and adaptation of the host. Ophiuroids, as the worldwide dominant benthos, have ecological roles in benthic-pelagic coupling in the sea floor. However, little is known about the composition and diversity of their gut microbiota and its potential functions in benthic ecosystems. In present study, we preformed 16S rRNA sequencing and function analysis in four dominant species (Stegophiura sladeni, Ophiopholis mirabilis, Ophiura sarsii vadicola, and Ophiura kinbergi) with two feeding types (suspension feeding/herbivores and scavenger/carnivores) from the Yellow Sea, China. Results showed that 56 phyla and 569 genera of microbiota were identified among ophiuroid guts. Multivariate and diversity analyses showed that the ophiuroid gut microbiota were independent and have higher biodiversity to the sediment microbial in the Yellow Sea. Phyla Proteobacteria, Firmicutes, Tenericutes, and Bacteroidetes were the dominant bacteria, with more than 80% abundance among the four ophiuroid species. A comparison among the gut microbial compositions among four ophiuroids showed the similarity of two offshore carnivore ophiuroids (S. sladeni and O. sarsii vadicola) and variation in the dominant microbiota types of three nearshore ophiuroids (S. sladeni, O. mirabilis, and O. kinbergi). The functional analysis revealed the significant differences of the environment-related expression in S. sladeni gut microbiota between nearshore and offshore environments. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional annotation showed the significant divergence of metabolism pathways between two nearshore species, the herbivores O. mirabilis and carnivores S. sladeni, such as the Lipid metabolism, Carbohydrate metabolism, and Metabolism of cofactors and vitamins. The homolog search and phylogenetic analysis identified the first gut symbiotic Candidatus Hepatoplasma in S. sladeni with important roles for the nutrient metabolisms. Overall, our study reported the comprehensive data of ophiuroid gut microbiota, while the functional microbiome provides insight into the physiology and environmental adaptation in ophiuroids.

Shifts of microbiota during cheese production: impact on production and quality

The high-throughput DNA sequencing (HTS) method is used to identify microbes in cheese and their potential functional properties. The technique can be applied to the microbiota of the cheese processing environment, raw milk, curd, whey, and starter cultures, and be used to improve the quality, safety, and other physicochemical properties of the final product. The HTS method is also utilized to study the microbiota shift of different types of cheeses during processing, as the composition and functional properties of the microbiome provide unique characteristics to different cheeses. Although there are several reviews that focused on microbiota of various types of cheeses, this review focuses on evaluating the microbiota shift of different types of cheese production and highlights key bacteria in each step of the processing as well as microbiota of various types of cheeses. KEY POINTS: • High-throughput sequencing can be applied to identify microbiota in cheese. • Microbiota in cheese is changed during making process and aging. • Starter culture plays an important role to establish microbiota in cheese.

Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization

Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.

Centennial glacier retreat increases sedimentation and eutrophication in Subantarctic periglacial lakes: A study case of Lake Uruguay

High resolution XRF scanning documented inter-annual paleolimnological changes of a Subantarctic periglacial lake, during a process of centennial glacier retreat in King George Island, Antarctica. Two major paleoenvironmental stages were inferred from the combined analysis of elemental, molecular and isotopic biomarkers, with a boundary or transition set at about 3200 yr BP. The first stage was characterized by a relatively low allochthonous organic content, reduced productivity and nitrogen levels. Such paleoenvironmental conditions are interpreted as a terrestrial system under periglacial influence, where material influx was related to erosion process from the melt water discharge, because of the proximity to the Collins Glacier ice cap. After the major Holocene glacier advance dated at about 3500 yr BP, the ice cap retreat led to the formation of Lake Uruguay, which involved in filling processes leading to moraine deposits, proglacial meltwater channels, and lakes next to the land glacier. During the second stage, with the onset of the Current Warm Period, prior to 1900 CE the stabilization of the Zr/Rb ratio within the laminated sediments documented the origin of the lacustrine sedimentation system, with subsequent increases in the sedimentation rate and biomass content (total nitrogen and organic carbon). Time series analyses revealed that the lake displayed variability cycles related to El Niño Southern Oscillation (ENSO), as reflected by high resolution sedimentological proxies for grain size, weathering, allochthonous inputs from the watershed, increase of biomass and productivity, and changes in redox conditions, all of which displayed similar oscillation cycles from 2 to 6 yr. During this periglacial recession and associated eutrophication process, we detected a striking loss in both bacterial specific richness and diversity as inferred from preliminary selected ancient DNA analyses. Thus, the Antarctic warming scenario leading to glacier depletion appears to exert deterioration consequences on the Subantarctic microbial web.

Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern

The solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually different microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in different vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon and nitrogen isotopic compositions determined from both mat samples showed that the δ¹³C_org and δ¹⁵N_org values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profile followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. The results and discussions presented here by merging culture-independent studies, predictive metabolic analyses and isotopic characterization, provide a collective strategy to understand the compositional and functional characteristics of microbial mats in saline environments.

Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils

Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.

Effects of Chitosan-Gentamicin Conjugate Supplement on Non-Specific Immunity, Aquaculture Water, Intestinal Histology and Microbiota of Pacific White Shrimp (Litopenaeus vannamei)

When the aquaculture water environment deteriorates or the temperature rises, shrimp are susceptible to viral or bacterial infections, causing a large number of deaths. This study comprehensively evaluated the effects of the oral administration of a chitosan-gentamicin conjugate (CS-GT) after Litopenaeus vannamei were infected with Vibrio parahaemolyticus, through nonspecific immunity parameter detection, intestinal morphology observation, and the assessment of microbial flora diversification by 16S rRNA gene sequencing. The results showed that the oral administration of CS-GT significantly increased total hemocyte counts and reduced hemocyte apoptosis in shrimp (p < 0.05). The parameters (including superoxide dismutase, glutathione peroxidase, glutathione, lysozyme, acid phosphatase, alkaline phosphatase, and phenoloxidase) were significantly increased (p < 0.05). The integrity of the intestinal epithelial cells and basement membrane were enhanced, which correspondingly alleviated intestinal injury. In terms of the microbiome, the abundances of Vibrio (Gram-negative bacteria and food-borne pathogens) in the water and gut were significantly reduced. The canonical correspondence analysis (CCA) showed that the abundances of Vibrio both in the water and gut were negatively correlated with CS-GT dosage. In conclusion, the oral administration of CS-GT can improve the immunity of shrimp against pathogenic bacteria and significantly reduce the relative abundances of Vibrio in aquaculture water and the gut of Litopenaeus vannamei.

Microbial community structures and functions of hypersaline heterotrophic denitrifying process: Lab-scale and pilot-scale studies

High-nitrate wastewaters are known pose substantial risks to human and environmental health, while their effective treatment remains difficult. The denitrification of saline, high-NO₃^- wastewaters was investigated at the laboratory- and pilot-scale experiment. Complete denitrification was achieved for three different realistic wastewaters, and the maximum influent [NO₃^-]₀ and salinity were as high as 20,500 mg/L and 7.8%, respectively. The results of microbial community structure analyses revealed that the sequences of denitrifying functional bacteria accounted for 96.2% of all sequences, and the functional genes for denitrification in bacteria were enriched with elevated salinity and [NO₃^-]₀. A significant difference was observed in the dominant bacterial genus between synthetic and realistic wastewaters. Thauera and Halomonas species evolved to be the most common dominant genera contributing to the processes of nitrate, nitrite, and nitrous oxide reductase. This study is practically valuable for the treatment of realistic, saline, high-NO₃^- wastewaters via denitrification by heterotrophic bacteria.

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

BACKGROUND

Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. In addition, there is also a lack of tools to predict functional gene redundancy in microbial communities.

RESULTS

To address these challenges, we developed Tax4Fun2, an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences. We demonstrate that functional profiles predicted by Tax4Fun2 are highly correlated to functional profiles derived from metagenomes of the same samples. We further show that Tax4Fun2 has higher accuracies than PICRUSt and Tax4Fun. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles is substantially enhanced. In addition, functional gene redundancies predicted with Tax4Fun2 are highly correlated to functional gene redundancies determined for simulated microbial communities.

CONCLUSIONS

Tax4Fun2 provides researchers with a unique tool to predict and investigate functional profiles of prokaryotic communities based on 16S rRNA gene sequencing data. It is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles. Another unique feature of Tax4Fun2 is that it allows researchers to calculate the redundancy of specific functions, which is a potentially important measure of how resilient a community will be to environmental perturbation. Tax4Fun2 is implemented in R and freely available at https://github.com/bwemheu/Tax4Fun2.

Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis

Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (i) assess the prokaryotic community composition of sponges from Zanzibar, (ii) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (iii) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.

Functional relationships between aboveground and belowground spinach (Spinacia oleracea L., cv. Racoon) microbiomes impacted by salinity and drought

Salinity is a major problem facing agriculture in arid and semiarid regions of the world. This problem may vary among seasons affecting both above- and belowground plant microbiomes. However, very few studies have been conducted to examine the influence of salinity and drought on microbiomes and on their functional relationships. The objective for the study was to examine the effects of salinity and drought on above- and belowground spinach microbiomes and evaluate seasonal changes in their bacterial community composition and diversity. Furthermore, potential consequences for community functioning were assessed based on 16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on results obtained with Piphillin. The experiment was repeated three times from early fall to late spring in sand tanks planted with spinach (Spinacia oleracea L., cv. Racoon) grown with saline water of different concentrations and provided at different amounts. Proteobacteria, Cyanobacteria, and Bacteroidetes accounted for 77.1% of taxa detected in the rhizosphere; Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil, while Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria accounted for 55.35% of taxa detected in the phyllosphere. Salinity significantly affected root microbiome beta-diversity according to weighted abundances (p = 0.032) but had no significant effect on the relative abundances of microbial taxa (p = 0.568). Pathways and functional genes analysis of soil, rhizosphere, and phyllosphere showed that the most abundant functional genes were mapped to membrane transport, DNA repair and recombination, signal transduction, purine metabolism, translation-related protein processing, oxidative phosphorylation, bacterial motility protein secretion, and membrane receptor proteins. Monoterpenoid biosynthesis was the most significantly enriched pathway in rhizosphere samples when compared to the soil samples. Overall, the predictive abundances indicate that, functionally, the rhizosphere bacteria had the highest gene abundances and that salinity and drought affected the above- and belowground microbiomes differently.

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis

The environment affects the composition and function of soil microbiome, which indirectly influences the quality of plants. In this study, 16S amplicon sequencing was used to reveal the differences in soil microbial community composition of Cistanche deserticola in three ecotypes (saline-alkali land, grassland and sandy land). Through the correlation analysis of microbial community abundance, phenylethanoid glycoside contents and ecological factors, the regulatory relationship between microbial community and the quality variation of C. deserticola was expounded. The metabolic function profile of soil microbiome was predicted using Tax4Fun. Data showed that the soil microbial communities of the three ecotypes were significantly different (AMOVA, P < 0.001), and the alpha diversity of grassland soil microbial community was the highest. Core microbiome analysis demonstrated that the soil microbial communities of C. deserticola were mostly have drought, salt tolerance, alkali resistance and stress resistance, such as Micrococcales and Bacillales. The biomarkers, namely, Oceanospirillales (saline-alkali land), Sphingomonadales (grassland) and Propionibacteriales (sandy land), which can distinguish three ecotype microbial communities, were excavated through LEfSe and random forest. Correlation analysis results demonstrated that 2'-acetylacteoside is positively correlated with Oceanospirillales in saline-alkali land soil. The metabolic function profiles displayed highly enriched metabolism (carbohydrate and amino acid metabolisms) and environmental information processing (membrane transport and signal transduction) pathways. Overall, the composition and function of soil microbiomes were found to be important factors to the quality variation of C. deserticola in different ecotypes. This work provided new insight into the regulatory relationship amongst the environment, soil microbial community and plant quality variation.

Age- and Sex-Linked Bacterial Community Variation and Function Prediction from Insoles of Healthy Chinese Population

Sweat secretion keeps feet and insoles humid and rich in nutrients, which are the conditions needed to maintain abundant microbial growth. Analyzing the diversity and function of microorganisms in the insole is of great significance in the development of functional insoles and prediction of human foot hygiene condition. In this study, pure culture method, MiSeq high-throughput sequencing technology, and PICRUSt gene function prediction were used to analyze the diversity and function of the bacterial community from insoles of healthy population of different sexes and age groups. Staphylococcus, Micrococcus, and Brevibacterium are present in all insole samples, and there is no significant difference between sexes of the same age group. However, a significant difference in insole microbial population was obtained among age groups. For community function, all six samples expressed similarity in the preliminary metabolism, but in samples from the elderly, many specific catabolic genes were associated with human disease and drug resistance. This study provides a reference for the development of multi-function insoles and other sanitary products for disease prediction in a healthy population.

Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis

In a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. savai, but it differs from them by some morphological and morphometric characters of the eggs. The p-distance between two COI haplotypes of Pam. experimentalis sp. nov. was 0.17%. In turn, the ranges of uncorrected genetic p-distances of all Paramacrobiotus species available in GenBank was from 18.27% (for Pam. lachowskae) to 25.26% (for Pam. arduus) with an average distance of 20.67%. We also found that Pam. experimentalis sp. nov. is bisexual. This observation was congruent on three levels: (i) morphological - specimen size dimorphism; (ii) structural (primary sexual characteristics) - females have an unpaired ovary while males have an unpaired testis and (iii) molecular - heterozygous and homozygous strains of the ITS-2 marker. Although symbiotic associations of hosts with bacteria (including endosymbiotic bacteria) are common in nature and these interactions exert various effects on the evolution, biology and reproductive ecology of hosts, there is still very little information on the bacterial community associated with tardigrades. To fill this gap and characterise the bacterial community of Pam. experimentalis sp. nov. populations and microbiome of its microhabitat, high throughput sequencing of the V3-V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed. The obtained 16S rRNA gene sequences ranged from 92,665 to 131,163. In total, 135 operational taxonomic units (OTUs) were identified across the rarefied dataset. Overall, both Pam. experimentalis sp. nov. populations were dominated by OTUs ascribed to the phylum Proteobacteria (89-92%) and Firmicutes (6-7%). In the case of samples from tardigrades' laboratory habitat, the most abundant bacterial phylum was Proteobacteria (51-90%) and Bacteroides (9-48%). In all compared microbiome profiles, only 16 of 137 OTUs were shared. We found also significant differences in beta diversity between the partly species-specific microbiome of Pam. experimentalis sp. nov. and its culturing environment. Two OTUs belonging to a putative bacterial endosymbiont were identified - Rickettsiales and Polynucleobacter. We also demonstrated that each bacterial community was rich in genes involved in membrane transport, amino acid metabolism, and carbohydrate metabolism.

Source Environments of the Microbiome in Perennially Ice-Covered Lake Untersee, Antarctica

Ultra-oligotrophic Lake Untersee is among the largest and deepest surface lakes of Central Queen Maud Land in East Antarctica. It is dammed at its north end by the Anuchin Glacier and the ice-cover dynamics are controlled by sublimation - not melt - as the dominating ablation process and therefore surface melt during austral summer does not provide significant amounts of water for recharge compared to subsurface melt of the Anuchin Glacier. Several studies have already described the structure and function of the microbial communities within the water column and benthic environments of Lake Untersee, however, thus far there have been no studies that examine the linkages between the lake ecosystem with that of the surrounding soils or the Anuchin Glacier. The glacier may also play an important role as a major contributor of nutrients and biota into the lake ecosystem. Based on microbial 16S rRNA amplicon sequencing, we showed that the dominant bacterial signatures in Lake Untersee, the Anuchin Glacier and its surrounding soils were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Aerosol and local soil depositions on the glacier surface resulted in distinct microbial communities developing in glacier ice and cryoconite holes. Based on a source tracking algorithm, we found that cryoconite microbial assemblages were a potential source of organisms, explaining up to 36% of benthic microbial mat communities in the lake. However, the major biotic sources for the lake ecosystem are still unknown, illustrating the possible importance of englacial and subglacial zones. The Anuchin Glacier may be considered as a vector in a biological sense for the bacterial colonization of the perennially ice-covered Lake Untersee. However, despite a thick perennial ice cover, observed "lift-off" microbial mats escaping the lake make a bidirectional transfer of biota plausible. Hence, there is an exchange of biota between Lake Untersee and connective habitats possible despite the apparent sealing by a perennial ice cover and the absence of moat areas during austral summer.

Enhancement of the removal and settling performance for aerobic granular sludge under hypersaline stress

The aerobic granular sludge (AGS) dominated by halophilic microorganisms, was successfully cultivated in a lab-scale sequencing batch reactor (SBR) under varying salinity levels (from 0% to 6% (w/v)). Removal performance of AGS improved with the increase of salinity and increased up to 42.86 mg g^-1 VSS h^-1 at 6% salinity. Increased salinity resulted in better settling performance of AGS in terms of the sludge volume index (SVI), which was initially 148.80 mL/g at 0% salinity and gradually decreased to 59.1 mL/g at 6% salinity. The increase of salinity stimulated bacteria to secret excessive extracellular polymeric substances (EPS), with its highest production of 725.5 mg/(g·VSS) at 5% salinity. The total protein (PN) exhibited highly positive correlation with the total EPS (R = 0.951), indicating that selective secretion of some functional PN played a key constituent in resisting the external osmotic pressure and improving sludge performance. Salinicola, accounted for up to 91% relative abundance at 6% salinity, showed the high positive correlation (R = 0.953) with salinity. The enrichment of such halophilic or halotolerant microbial community assured both stable and improved removal performance in the AGS system. The enrichment of salt response pathways and altered metabolic processes for salt-tolerant bacteria indicated that the microbial community formed special metabolic pattern under long-term hypersaline stress to maintain favourable cellular activity and removal performance.

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F-1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.

How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities

Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.

Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences

The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.

Dysbiosis and early mortality in zebrafish larvae exposed to subclinical concentrations of streptomycin

Exposure to low concentrations of antibiotics found in aquatic environments can increase susceptibility to infection in adult fish due to microbiome disruption. However, little is known regarding the effect of antibiotic pollution on fish larvae. Here, we show that exposure to streptomycin, a common antibiotic used in medicine and aquaculture, disrupts the normal composition of zebrafish larvae microbiomes, significantly reducing the microbial diversity found in the fish. Exposure to streptomycin also significantly increased early mortality among fish larvae, causing full mortality within a few days of exposure at 10 μg/mL. Finally, we found that subclinical concentrations of streptomycin also increased the abundance of class 1 integrons, an integrase-dependent genetic system associated to the horizontal transfer of antibiotic resistance genes, in the larvae microbiomes. These results suggest that even low concentrations of streptomycin associated with environmental pollution could impact fish populations and lead to the creation of antibiotic resistance reservoirs.

Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.