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This thesis investigated the effects of multi species grassland mixtures on the composition and function of the soil microbiome in temperate grasslands. Three major gaps in knowledge were identified: (1) What effects do multi species swards have on the composition, diversity and nitrogen cycling capabilities of the soil microbiome? (2) What effects do multi species swards have on the resistance and resilience of the soil microbiome to drought, in terms of composition, diversity and nitrogen cycling potential? (3) What effects do deep rooting plants in multi species swards have on the composition, diversity and carbon cycling capabilities of the soil microbiome? Plant identity was a major determinant of microbial diversity, abundance and function in the soil, while plant interspecific species interactions generally had no effect. Soil microbial community abundance, composition and nitrogen cycling functions were generally resistant and resilient to drought, regardless of plant identity. However, where vulnerability to drought was observed, drought resistance and resilience was in many cases mediated by plant identity. In contrast, plant interspecific species interactions generally had no influence on soil microbial drought resistance and resilience. 300N L. perenne monocultures were less resistant and resilient to drought, suggesting over fertilisation can make grasslands more vulnerable to climatic stress. Soil microbial abundance and carbon cycling function decreased, and community composition changed, along the soil depth gradient, regardless of plant identity. Plant identity significantly influenced 16S microbial community composition in the top 15cm of soil and fungal community composition between 15-30 cm in soil. Carbon cycling enzymes were significantly more active at depth when deep rooting plant species were present. This work will contribute significantly to the knowledge of microbial diversity and function in species diverse grasslands, and help provide evidence-based advice for maintaining productive and sustainable agricultural grassland systems in the face of changing global climates.

Dietary fiber plays an important role in porcine gut health and welfare. Fiber is degraded by microbial fermentation in the intestine, and most gut microbiota related to fiber digestibility in pigs are worth pursuing. The aim of this study was to identify gut microbiota associated with the apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF) and of acid detergent fiber (ADF) in pigs. Large phenotypic variations in the ATTD of NDF and of ADF were separately found among 274 Suhuai pigs. Microbial community structures were significantly different between high and low fiber digestibility groups. Fourteen genera separately dominated the communities found in the high ATTD (H-AD) of NDF and ADF samples and were in very low abundance in the low ATTD (L-AD) of NDF and ADF samples. In conclusion, norank_f__Bacteroidales_S24-7_group (p < 0.05), Ruminococcaceae_UCG-005 (p < 0.05), unclassified_f__Lachnospiraceae (p < 0.05), Treponema_2 (p < 0.01), and Ruminococcaceae_NK4A214_group (p < 0.01) were the main genera of gut microbiota affecting the ATTD of NDF in pigs. Christensenellaceae_R-7_group (p < 0.01), Treponema_2 (p < 0.05), Ruminococcaceae_NK4A214_group (p < 0.05), Ruminococcaceae_UCG-002 (p < 0.05), and [Eubacterium]_coprostanoligenes_group (p < 0.05) were the main genera of gut microbiota affecting the ATTD of ADF in pigs. The most important functions of the above different potential biomarkers were: carbohydrate transport and metabolism, general function prediction only, amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, translation, transcription, replication, energy production and conversion, signal transduction mechanisms, and inorganic ion transport and metabolism. The most important metabolic pathways of the above different potential biomarkers were: membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, cell motility, energy metabolism, poorly characterized, nucleotide metabolism, metabolism of cofactors and vitamins, and cellular processes and signaling.

The microbial characteristics of water treated by tea polyphenols after the ultrafiltration process were studied based on the continuous disinfection performance of tea polyphenols. Metagenomics was carried out to investigate the microbial community distribution, functional characteristics, and variations after disinfection, to reveal the disinfection principle of tea polyphenols, and to provide the theoretical basis for using tea polyphenols as a disinfectant to better control the growth of microorganisms. The analysis of microbial diversity and community structure showed that the microbial diversity in water was significantly reduced after disinfection with tea polyphenols. The results of hierarchical clustering analysis showed that microbial metabolism, environmental information processing, and functional modules in genetic information processing were significantly inhibited after disinfection treatment using tea polyphenols. The tea polyphenols inhibit the growth and reproduction of microorganisms by selection on the microorganisms in the water, thus achieving the effect of bacterial inhibition. HIGHLIGHTS Tea polyphenols as disinfectants inhibit the regrowth of bacteria.; Tea polyphenols disinfection significantly reduces the diversity of microorganisms in water.; The gene function of many microorganisms in water is greatly changed after disinfection by tea polyphenols.; Tea polyphenols disinfection exerts a greater inhibitory effect on the metabolism of various nucleotides and related processes of microorganisms.

Ozone is a typical hazardous pollutant in Earth’s lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research to explore the efficiency and mechanism of ozone phylloremediation, the response and role of the phyllosphere microbiome remains untouched. In this study, we exposed Euonymus japonicus to different ozone levels and revealed microbial successions and roles of the phyllosphere microbiome during the exposure. The low-level exposure (156 ± 20 ppb) induced limited response compared to other environmental factors. Fungi failed to sustain the community richness and diversity, despite the stable ITS concentration, while bacteria witnessed an abundance loss. We subsequently elevated the exposure level to 5000~10,000 ppb, which considerably deteriorated the bacterial and fungal diversity. Our results identified extremely tolerant species, including bacterial genera (Curtobacterium, Marmoricola, and Microbacterium) and fungal genera (Cladosporium and Alternaria). Compositional differences suggested that most core fungal taxa were related to plant diseases and biocontrol, and ozone exposure might intensify such antagonism, thus possibly influencing plant health and ozone remediation. This assumption was further evidenced in the functional predictions via a pathogen predominance. This study shed light on microbial responses to ozone exposure in the phyllosphere and enlightened the augmentation of ozone phylloremediation through the microbial role.

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstonia pickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, Candidatus Competibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonas aquatilis and Roseomonas gilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridium sensu stricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

Reductive soil disinfestation (RSD) is an effective practice to eliminate plant pathogens and improve the soil microbial community. However, little is known about how RSD treatment affects microbial interactions and functions. Previous study has shown that RSD-regulated microbiomes may degenerate after re-planting with former crops, while the effect of planting with different crops is still unclear. Here, the effects of both RSD treatment and succession planting with different crops on microbial community composition, interactions, and functions were investigated. Results showed that RSD treatment improves the soil microbial community, decreases the relative abundance of plant pathogens, and effectively enhances microbial interactions and functions. The microbial network associated with RSD treatment was more complex and connected. The functions of hydrocarbon (C, H), nitrogen (N), and sulfur (S) cycling were significantly increased in RSD-treated soil, while the functions of bacterial and fungal plant pathogens were decreased. Furthermore, the bacterial and fungal communities present in the RSD-treated soil, and soil succession planted with different crops, were found to be significantly different compared to untreated soil. In summary, we report that RSD treatment can improve soil quality by regulating the interactions of microbial communities and multifunctionality.

High throughput sequencing of gut microbiota helps to understand the nutrition and health of the host. In this sense, it is an important tool for improving wildlife conservation and management. Little is known about the microbial communities occupying the gastrointestinal tract and the differences of microbiota among primate species. We conducted a microbiome study of the gastrointestinal tract in golden snub-nosed monkey (Rhinopithecus roxellanae), green monkey (Chlorocebus aethiops sabaeus), and ring-tailed lemur (Lemur catta), using the 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. The gastrointestinal tract of all three primates were characterized by Firmicutes, Bacteroidetes, and Proteobacteria, although the relative abundance of these taxa differed across non-human primate species and gastrointestinal segments. In addition, the stomach of the golden monkey demonstrated a strong signal of microbial metabolic activity, especially in metabolizing carbohydrate. Prevotella multisaccharivorax and Selenomonas bovis were the main contributors to the function, and the enzymes involved in these metabolic activities were mainly derived from the glycoside hydrolase (GH) family. Microbial composition and function vary widely across non-human primate species and gastrointestinal segments. Therefore, while faecal samples are necessary for studying many mammals, particularly in the wild, data from the gastrointestinal tract have the potential to greatly improve our knowledge of host-gut microbe interactions. This information can contribute to the development of conservation interventions and animal care protocols in the wild and captivity to more fully describe a species’ nutritional needs and advance health and survival.

Feed efficiency is a highly important economic trait in sheep production and has a significant impact on the economic benefits of sheep farming. Microbial fermentation of the rumen has a vital role in the host's nutrition; the rumen microbiota might affect host feed efficiency. However, the relationship between the rumen microbiota and feed efficiency in sheep is unclear. In the present study, the microbiota of 195 Hu sheep was investigated and their residual feed intake (RFI), a commonly used measure of feed efficiency, was determined. From birth, all sheep were subjected to the same management practices. At slaughter, samples of liquid rumen contents were collected and subjected to amplicon sequencing for the 16S rDNA gene on the IonS5™XL platform. To identify the bacterial taxa differentially represented at the genus or higher taxonomy levels, we used linear discriminant analysis coupled with effect size and curve fitting. In the sheep rumen, the four most abundant phyla were Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria; and the dominant genera were unidentified Prevotellaceae, Fibrobacter, unidentified Lachnospiraceae, Saccharofermentans, and Succinivibrio. Pathway analysis of the 16S rDNA sequencing data from the rumen microbiota identified that carbohydrate metabolism was enriched. Using α-diversity analysis, we further identified that Observed species, ACE, Good's coverage, and Chao1 are more abundant (P

Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.

The role of gastrointestinal microbiome has long been proven to be crucial in the nutrition uptake and metabolism of host. In paddlefish (Polyodon spathula), a greater proportion of Gammaproteobacteria, Fusobacteriia, Clostridia, Alphaproteobacteria were found in esophagus and stomach, whereas intestine was predominated by Fusobacteriia, Gammaproteobacteria, and Bacteroidia detected by 16s RNA sequencing. Shannon diversity index and microbial richness decreased along the digestive tract, and a significantly higher proportion of Cetobacterium was observed in intestine, following by a remarkable alteration in the structure of microbial community in intestine compared to esophagus and stomach. Through species-species interactions, microbiome formed unique ecological networks to adapt the distinct physicochemical conditions in esophagus, stomach, and intestine, and dominant microflora was the major component of these networks. Within these networks, many bacterial strains from the dominant microbiota served important ecological roles such as module hubs or connectors, which contributed in maintaining the stability of the microbial community. The microbial cooperative interactions predominated along the digestive tract, and the lowest proportion of competitive interactions was observed in stomach. Microbial function composition in intestine, predicted by function analysis, significantly differed from that in esophagus and stomach. Specially, in terms of nutrition metabolism, the intestinal microbial community exhibited a high capacity in carbohydrate fermentation compared with that in esophagus and stomach. These results suggested that the microbial composition and function in intestine were significantly different from that in esophagus and stomach of paddle fish. Moreover, complex species-species interactions may promote the adaptation of microbiome to the physiological environment of the host.

Microbial diversity and function in intermittent rivers and ephemeral streams (IRES) are tightly linked to specific habitat availability and hydrological phases. The intensity and frequency of the different phases (especially drying and rewetting) affect community composition and key functions, mainly linked to biogeochemical processes. Resistance and resilience strategies are distinct among microorganism groups-bacteria, archaea, fungi, protozoans-and strongly depend on different types of microhabitat or refuge available. The biodiversity of prokaryotes in IRES is strongly affected by hydrology but microhabitat conditions and type of benthic substrate significantly affect their community composition. Fungi are very sensitive to drying but use several refuges, including the terrestrial habitat, and resistance strategies. Protozoans show a wide range of survival strategies and several species can resist harsh conditions such as anoxia in drying pools. Thus, they become especially relevant for ecosystem functions when other organisms are inhibited. This sensitivity causes "waves" of microbial functions and biodiversity to covary with hydrological phases, potentially affecting ecosystem functioning and higher trophic levels. Microbially mediated functions in IRES are perhaps the most critical to freshwater ecosystem services such as nitrogen and carbon cycling. Therefore, efforts to manage and restore IRES will depend on improved understanding of hydrological controls on microbial communities and functions across space and time. © 2017 Copyright

The effect of organic amendments and pesticides on a soil microbial community has garnered considerable interest due to the involvement of microorganisms in numerous soil conservation and maintenance reactions. The aim of this work was to assess the influence on a soil microbial community of the simultaneous application of the herbicide triasulfuron at three doses (2, 10, and 50 mg kg-1), with an organic amendment [sewage sludge (SS) or green compost (GC)]. Dissipation kinetics, soil microbial biomass, dehydrogenase activity (DHA) and respiration, and the profile of phospholipid fatty acids (PLFAs) extracted from the soil, were determined in unamended (S) soil and amended (S+SS and S+GC) ones. Triasulfuron dissipation followed the single first-order kinetics model. Half-life (DT50) values were higher in the amended soils than in the unamended one for the 10 and 50 mg kg-1 doses. The dissipation rates were lower in the S+GC soil for the three herbicide doses applied. In general, soil biomass, DHA and respiration values increased in SS- and GC-amended soils compared to the unamended one. DHA values decreased (S and S+SS) or increased (S+GC) with the incubation time of soil with herbicide at the different doses applied. Respiration values increased with the herbicide doses applied and decreased with the incubation time, although maximum values were obtained for soils treated with the highest dose after 70 days of incubation. PLFA analysis indicated different effects of triasulfuron on the soil microbial community structure depending on the organic amendments. While the increasing triasulfuron doses resulted in deeper alterations in the S soil, the time after triasulfuron application was the most important variation in the S+SS and S+GC soils. The overall results indicate that the soil amendment has an effect on herbicide dissipation rate and the soil microbial community. Initially, a high dose of triasulfuron had detrimental effects on the soil microbial community, which is important in the case of the long-term use of this compound., This work was supported by the “Junta de Castilla y León” (project CSI264A12-1 and CSI240U14). EP-J was supported by a postdoctoral contract (Juan de la Cierva JCI-2011-10150) from the Spanish Ministry of Science and Innovation.

Background. Tetracycline is a widely used antibiotic in animal production. Significant amounts of the substance reach the soil via feces, urine and manure application. As tetracycline is a persistent compound with antibacterial activity, its presence in soil may have undesired direct and indirect effects. These have been investigated so far focusing on effects on selected microbial functions. Objectives. The aim of the present study was to obtain comprehensive information on potential effects of tetracycline on the soil microflora under environmentally relevant conditions. The investigations included function and structure of the microbial biocoenosis and the distribution of resistance genes. Methods. Pig manure rich in tetracycline resistance genes was applied to a sandy soil. This soil as well as an unamended soil were additionally treated with several concentrations of tetracycline. The spiked soils were incubated in outdoor lysimeters for several month. Substrate induced respiration, PLFAs, ten selected resistance genes, and the concentrations of tetracycline were determined. Results. The test concentrations, through far exceeding environmental relevance, caused only small effects. An establishment of resistance could not be detected. Applied resistance genes were not detectable at the end of the study even in the presence of added tetracycline. Conclusion. Due to the high sorption capacity of the antibiotic, environmentally relevant concentrations of tetracycline do not seem to cause undesired effects on the soil microflora.