Following bowel surgery, infectious complications, including anastomotic leak (AL), remain major sources of morbidity and mortality. Bowel preparation is often administered with the assumption that gut decontamination reduces post-surgical complications. In this study, we tested this hypothesis using a murine model of colon surgery. The mice were fed either regular chow or a high-fat, high-sugar Western diet. The day before surgery, the mice received one of four interventions: water (control), mechanical bowel preparation (MBP), oral antibiotics (OA), or both MBP and OA. We found no differences in the rates of AL among the experimental groups, and diet did not appear to affect the outcomes. Exploratory analyses showed changes in the gut microbiome consistent with the different treatments, but investigations of fecal short-chain fatty acids and RNA sequencing of colonic tissue did not reveal specific effects of the treatments or the presence of AL. However, we did identify bacterial genera that may be causally associated with AL and developed a predictive index from stool samples as a marker for the presence of AL. Future research is needed to identify and validate a microbial predictive tool and to uncover the microbial-driven mechanisms that lead to AL.

Host diet and gut microbiota interact to contribute to perioperative complications, including anastomotic leak (AL). Using a murine surgical model of colonic anastomosis, we investigated how diet and fecal microbial transplantation (FMT) impacted the intestinal microbiota and if a predictive signature for AL could be determined. We hypothesized that a Western diet (WD) would impact gut microbial composition and that the resulting dysbiosis would correlate with increased rates of AL, while FMT from healthy, lean diet (LD) donors would reduce the risk of AL. Furthermore, we predicted that surgical outcomes would allow for the development of a microbial preclinical translational tool to identify AL. Here, we show that AL is associated with a dysbiotic microbial community characterized by increased levels of Bacteroides and Akkermansia. We identified several key taxa that were associated with leak formation, and developed an index based on the ratio of bacteria associated with the absence and presence of leak. We also highlight a modifiable connection between diet, microbiota, and anastomotic healing, potentially paving the way for perioperative modulation by microbiota-targeted therapeutics to reduce AL.

Lung group 2 innate lymphoid cells (ILC2s) control the nature of immune responses to airway allergens. Some microbial products, including those that stimulate interferons, block ILC2 activation, but whether this occurs after natural infections or causes durable ILC2 inhibition is unclear. In the present study, we cohoused laboratory and pet store mice as a model of physiological microbial exposure. Laboratory mice cohoused for 2 weeks had impaired ILC2 responses and reduced lung eosinophilia to intranasal allergens, whereas these responses were restored in mice cohoused for ≥2 months. ILC2 inhibition at 2 weeks correlated with increased interferon receptor signaling, which waned by 2 months of cohousing. Reinduction of interferons in 2-month cohoused mice blocked ILC2 activation. These findings suggest that ILC2s respond dynamically to environmental cues and that microbial exposures do not control long-term desensitization of innate type 2 responses to allergens.

The intestinal microbiota produces β-glucuronidase that plays an essential role in the metabolism of the immunosuppressant mycophenolate mofetil (MMF). This drug is commonly used in organ and hematopoietic cell transplantation (HCT), with variations in dosing across transplant types. We hypothesized that β-glucuronidase activity differs between transplant types, which may account for differences in dosing requirements. We evaluated fecal β-glucuronidase activity in patients receiving MMF post-allogeneic HCT and post-kidney transplant. Kidney transplant patients had significantly greater β-glucuronidase activity (8.48 ± 6.21 nmol/hr/g) than HCT patients (3.50 ± 3.29 nmol/hr/g; P = .001). Microbially mediated β-glucuronidase activity may be a critical determinant in the amount of mycophenolate entering the systemic circulation and an important factor to consider for precision dosing of MMF.

Earthworms have the remarkable capability of decomposing the organic matter through a biochemical oxidative process popularly called as vermicomposting. As this process significantly alters the physical and biochemical attributes of organic matter through solubilization of minerals, the resultant product called vermicompost is highly rich in nutrients that are very useful for improving the soil fertility. The organic matter decomposition is mainly carried out by microorganisms, while the earthworms provide a milieu favorable for activity of microorganisms, through ingestion and churning of the organic matter. Hence, investigation on the pattern of changes taking place in the community of microorganisms during vermicomposting is very important as it has a direct bearing on vermicompost quality. With the advancement in tools and techniques for scientific research on vermicomposting, our understanding about the entire process has tremendously increased over past few decades. Of particular relevance, here are the molecular tools and techniques that have greatly enhanced our knowledge in understanding the microbial community dynamics of vermicomposting. This chapter provides an overview of molecular tools and techniques being used for unravelling the mechanisms of interactions of microorganisms with various biotic and abiotic factors under a unique micro-ecosystem where the earthworms are crucial drivers of the process owing to their active role in the stimulation of microbial populations.

Plant growth-promoting rhizobacteria (PGPR) improve plant health under various biotic and abiotic stresses. However, the underlying mechanisms of the protective effects of PGPR in deficit water stress (WS) remain less explored. This study aimed to characterize the role of Ochrobactrum sp. NBRISH6 inoculation on maize (Zea mays "Maharaja") under WS conditions using multiple approaches such as physiological, anatomical, metabolic, and molecular. The effect of NBRISH6 inoculation using maize as a host plant was characterized under greenhouse conditions in deficit water stress. Results from this study demonstrated that NBRISH6 significantly lowered the expression of genes involved in the abscisic acid cycle, deficit water stress-response, osmotic stress, and antioxidant enzyme activity (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and polyphenol oxidase). Phytohormones, i.e. indole acetic acid (IAA) and salicylic acid (SA) levels, intercellular CO2 concentration, metabolites such as simple sugars, amino acids, aliphatic hydrocarbons, and the number of shrunken pith cells modulated in maize roots inoculated with NBRISH6. The NBRISH6 inoculation also improved the plant vegetative properties (root length, 33.80%; shoot length, 20.68%; root dry weight, 39.21%; shoot dry weight, 61.95%), shoot nutrients, xylem cells, root hairs, vapor pressure deficit (75%), intrinsic water-use efficiency (41.67%), photosynthesis rate (83.33%), and total chlorophyll (16.15%) as compared to the respective stress controls. This study provides valuable insights into mechanistic functions of PGPR in WS amelioration and promoting plant physiological response.

Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe-related traits were developed in the relatively simple context of binary host-microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome-wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant-microbe interactions will influence the choice of traits to be mapped.

The current study was carried out for the purpose of comparative evaluation of vegetable market waste degradation potential of three earthworm species (Eisenia fetida, Perionyx excavatus and Eudrilus eugeniae). The vegetable waste used as substrate in this study was collected from Mission Chariali vegetable market in Tezpur, Assam, India. Non-biodegradable materials such as polythenes, plastic etc. were segregated and organic waste was sun-dried. Cow dung was mixed with the substrate in 1:3 proportion and subjected to vermicomposting with three earthworms species separately. The data on physicochemical properties of the compost bed along with earthworm activity were collected every 10 days interval. The experiment was continued until 70 days. Analysis of the data indicated that E. fetida posed maximal nutrient mineralization and reduction in C:N ratio when compared with the data of day 0 with of day 70. Also, the values of vermicomposting coefficient were maximum for E. fetida. Moreover, the mean individual weight of E. fetida was also maximum during the decomposition period. Although Eu. eugeniae increased in total biomass much more rapidly than E. fetida, nevertheless, the cocoon production rate was greatest (78.67) in case of E. fetida, indicating the differential resource allocation with trade-off between sex alloca-tion and growth by Eu. eugeniae in a non-conducive environment during its life cycle. Overall, the results indicate suitability of E. fetida for vegetable waste degradation.

A comprehensive survey for 09 agro-climatic zones of Uttar Pradesh, India was conducted to isolate and characterize salt tolerant 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase possessing plant growth promoting (PGP) rhizobacteria for salt stress amelioration in rice. Here, we have isolated 1125 bacteria having the ability to tolerate 1M NaCl and out of those, 560 were screened for utilizing ACC as sole nitrogen source. 560 isolates were subjected for bacteria coated seed germination assay under 100mM salt (NaCl) stress resulting to 77 isolates which were further evaluated for seed germination assay, PGP and abiotic stress tolerance ability in vitro. This evaluation revealed 15 potent rhizobacteria representing each agro-climatic zone and salt stress mitigation in vitro. In particular, the biomass obtained for bacteria coated rice seedlings were corroborated with the performance of isolates exhibiting maximum average indole acetic acid (IAA) production respective to the agro-climatic zone. Surprisingly based on 16S rRNA, much of the propitious isolates belonged to same specific epithet exhibited variedly in their characteristics. Overall, Bacillus spp. was explored as dominant genera in toto with highest distribution in Western Plain zone followed by Central zone. Therefore, this study provides a counter-intuitive perspective of selection of native microflora for their multifarious PGP and abiotic stress tolerance abilities based on the agro-climatic zones to empower the establishment and development of more suitable inoculants for their application in agriculture under local stress environments.

Emerging environmental issues related to heavy metal contamination in rice draw great concern about the soil quality of paddy farming lands irrigated with groundwater. Investigating the functioning of soil microorganisms exposed to heavy metal contamination is imperative for agricultural soil manipulations. The current study accentuates the influence of heavy metals on microbial activity and community composition in arable soil of West Bengal State of India. The result revealed that the fertility indicators (activity of all soil enzymes) and growth-limiting factors (soil N and P) were negatively correlated with the heavy metal stress except the soil total organic content which demonstrated significant positive correlation with the heavy metals. In case of functional diversity of soil, all the considered diversity indices exhibited no specific pattern along with the availability of heavy metals. Further, despite the heavy metal contamination, we observed a very complex and indifferent pattern of bacterial community composition along the heavy metal contamination sites. Overall, we found that γ-Proteobacteria had been the most abundant bacterial community followed by Actinobacteria, Firmicutes, β-Proteobacteria and α-Proteobacteria. Commemorating all the results, we can infer that arsenic and other heavy metal contamination is deteriorating the soil quality and hence warrants immediate attention of concerned soil scientist and agronomists.

Soil bacteria may have properties of plant growth promotion but not be sufficiently beneficial for plants under stress conditions. This challenge has led researchers to extend their searches into extreme environments for potential soil bacteria with multiple plant beneficial traits as well as abiotic stress tolerance abilities. In the current study, an attempt was made to evaluate soil bacteria from an extreme environment, volcano soils, based on plant growth promoting and abiotic stress mitigating characteristics. The screening led to the isolation of eight (NBRISH4, NBRISH6, NBRISH10, NBRISH11, NBRISH13, NBRISH14, NBRISH16 and NBRISH26) bacterial isolates capable of withstanding stresses, namely temperature (up to 45 °C), salt (up to 2 M NaCl) and drought (up to 60% Poly Ethylene Glycol 6000) in vitro. Further, the selected isolates were notable for their in vitro temporal performance with regards to survival (in terms of colony count), phosphate solubilisation, biofilm formation, auxin, alginate and exo-polysaccharide production abilities under abiotic stresses i.e. 40 °C temperature; 500 mM NaCl salt and drought (PEG) conditions. In vivo seed treatments of individual selected bacteria to maize plants resulted into significant enhancement in root and shoot length, root and shoot fresh and dry weight and number of leaves per plant. Overall, the plant growth promoting and abiotic stress tolerance ability was most evident for bacterial isolate NBRISH6 which was identified as an Ochrobactrum sp. using 16S rRNA based phylogenetic analysis.

In India and other developing countries, management of the urban solid waste is one of the most neglected areas of urban development. In addition, the continuous and indiscriminate use of easily soluble chemical fertilizers in high doses in agriculture has been found to be one of the major factors con-tributing to soil deterioration. Incidentally, earthworms have remarkable capability of effectively degrading waste biomass into vermicompost as their excreta. A major proportion of municipal solid waste generated is organic, which can be used as substrate for vermicomposting thereby minimizing pressure on the landfill sites. As the vermicompost application can significantly improve the soil fertility and in-turn plant health, the potential of earthworms in agriculture was realized soon and they became farmers’ friend. The modern researchers identified the environmental conditions optimal for earthworm activity for their effective utilization in organic waste degradation. Despite the worthwhile significance of vermibiotechnology in mu-nicipal solid waste management and in sustainable agriculture, it has not yet reached effectively to the stakeholders. This review attempts to elaborate the relevance of vermibiotechnology in Indian context for solid waste man-agement and in agriculture. Further, various challenges with respect to using this technology are highlighted. After detailed and critical analysis of the existing scientific literature, we also discuss future prospects of vermibi-otechnology in Indian context.

The functioning of high-altitude agro-ecosystems is constrained by the harsh environmental conditions, such as low temperatures, acidic soil, and low nutrient supply. It is therefore imperative to investigate the site-specific ecological stoichiometry with respect to AM symbiosis in order to maximize the arbuscular mycorrhizal (AM) benefits for the plants in such ecosystems. Here, we assess the elemental stoichiometry of four Capsicum genotypes grown on acidic soil at high altitude in Arunachal Pradesh, India. Further, we try to identify the predominant resource limitations influencing the symbioses of different Capsicum genotypes with the AM fungi. Foliar and soil elemental stoichiometric relations of Capsicum genotypes were evaluated with arbuscular mycorrhizal (AM) colonization and occurrence under field conditions. AM fungal diversity in rhizosphere, was estimated through PCR-DGGE profiling. Results demonstrated that the symbiotic interaction of various Capsicum genotypes with the AM fungi in acidic soil was not prominent in the study site as evident from the low range of root colonization (21–43.67%). In addition, despite the rich availability of carbon in plant leaves as well as in soil, the carbon-for-phosphorus trade between AMF and plants appeared to be limited. Our results provide strong evidences of predominant influence of the potassium-limitation, in addition to phosphorus-limitation, on AM symbiosis with Capsicum in acidic soil at high altitude. We also conclude that the potassium should be considered in addition to carbon, nitrogen, and phosphorus in further studies investigating the stoichiometric relationships with the AMF symbioses in high altitude agro-ecosystems.

Vermiwash (VW), a liquid extract obtained from vermicomposting beds, is used as an organic fertilizer for crop plants. The current study investigated the effect of a vermiwash foliar spray on the response of bhut jolokia (Capsicum assamicum) exposed to two different arbuscular mycorrhizal fungi (AMF: Rhizophagus irregularis, RI and G. mosseae, GM) in acidic soil under naturally ventilated greenhouse conditions. The VW spray significantly influenced the growth of plants receiving the dual treatment of AMF+VW. Plant growth was more prominent in the GM+VW treatment group than that in the RI+VW treatment group. The plant-AMF interactions in relation to growth and nutrient requirements were also significantly influenced by the application of VW. Interestingly, the VW treatment appeared to contribute more N to plants when compared to that under the AMF treatment, which led to changes in the C:N:P stoichiometry in plant shoots. Furthermore, the increased potassium dependency, as observed in the case of the dual treatments, suggests the significance of such treatments for improving crop conditions under salt stress. Overall, our study shows that the VW foliar spray modifies the response of a crop to inoculations of different AMF with regard to growth and nutrient utilization, which has implications for the selection of an efficient combination of nutrient source for improving crop growth.

Northeastern India is one of the most important biodiversity hotspots in the world. However, hot and humid climatic conditions of the region favor growth and development of foliar fungal phytopathogens such as cercosporoid fungi. The genus Cercospora is one of the largest genera of hyphomycetes. Species of Cercospora are known to cause leaf spot disease in several cultivated and non-cultivated plants leading to considerable losses. In this study, we describe a new species of Cercospora which was isolated from the leaves of Naga chilli (Capsicum assamicum Purkayastha & Singh) grown in northeastern India. Comparison of the detailed morphological characteristics along with the DNA sequences for four gene regions, namely actin, calmodulin, histone H3 and translation elongation factor-1α of this isolate, was made with those of some previously reported Cercospora species infecting Capsicum and other similar species of Cercospora from other hosts. The results suggested that our isolate represents an undescribed taxon and warrants the establishment of a new species, Cercospora tezpurensis sp. nov.