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Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over three years. The system comprised two fishponds, where fish are grown, and a “control” operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects if aquaculture-related factors.HighlightsWe present three years of monthly microbiome data from an aquaculture facility.The microbiome changes seasonally, likely driven by temperature and rainwater runoff.Summer blooms of toxin-producing cyanobacteria are repeatedly observed.Fish food may impact microbiome through changes in nutrient ratios.

Actinomycetes represent important microbial communities in the soils and inhabit very high proportion of soil microbial biomass that has the capacity to produce a wide range of high-value antibiotics, organic acids, phytohormones, extracellular enzymes, bioactive compounds, and secondary metabolites other than antimicrobials. Several strains of actinomycetes were found to promote plant growth directly and protect plants against phytopathogens and plant pests. The potential of this important microbial community for agricultural productivity is being greatly realized because they are a good source for agroactive compounds, plant growth-promoting substances, and biocontrol tools of the control of plant diseases. This chapter describes certain important aspects of actinomycetes in plant growth promotion and biological control.

The genus Aeromonas is ubiquitous in aquatic environments encompassing a broad range of fish and human pathogens. Aeromonas strains are known for their enhanced capacity to acquire and exchange antibiotic resistance genes and therefore, are frequently targeted as indicator bacteria for monitoring antimicrobial resistance in aquatic environments. This study evaluated temporal trends in Aeromonas diversity and antibiotic resistance in two adjacent semi-intensive aquaculture facilities to ascertain the effects of antibiotic treatment on antimicrobial resistance. In the first facility, sulfadiazine-trimethoprim was added prophylactically to fingerling stocks and water column-associated Aeromonas were monitored periodically over an 11-month fish fattening cycle to assess temporal dynamics in taxonomy and antibiotic resistance. In the second facility, Aeromonas were isolated from fish skin ulcers sampled over a 3-year period and from pond water samples to assess associations between pathogenic strains to those in the water column. A total of 1200 Aeromonas isolates were initially screened for sulfadiazine resistance and further screened against five additional antimicrobials. In both facilities, strong correlations were observed between sulfadiazine resistance and trimethoprim and tetracycline resistances, whereas correlations between sulfadiazine resistance and ceftriaxone, gentamicin, and chloramphenicol resistances were low. Multidrug resistant strains as well as sul1, tetA, and intI1 gene-harboring strains were significantly higher in profiles sampled during the fish cycle than those isolated prior to stocking and these genes were extremely abundant in the pathogenic strains. Five phylogenetically distinct Aeromonas clusters were identified using partial rpoD gene sequence analysis. Interestingly, prior to fingerling stocking the diversity of water column strains was high, and representatives from all five clusters were identified, including an A. salmonicida cluster that harbored all characterized fish skin ulcer samples. Subsequent to stocking, diversity was much lower and most water column isolates in both facilities segregated into an A. veronii-associated cluster. This study demonstrated a strong correlation between aquaculture, Aeromonas diversity and antibiotic resistance. It provides strong evidence for linkage between prophylactic and systemic use of antibiotics in aquaculture and the propagation of antibiotic resistance.

Six actinomycetes isolates, namely Streptomyces toxytricini vh6, Streptomyces flavotricini vh8, S. toxytricini vh22, Streptomyces avidinii vh32, Streptomyces tricolor vh85 and vh41, an isolate of an unknown species of Actinomycetales, were tested for their efficacy in protecting tomato (Solanum lycopersicum) against Rhizoctonia solani under green house conditions. Actinomycetes treated plants showed better growth in terms of high chlorophyll content, higher phenylalanine ammonia lyase (PAL) activity and high total phenolic content. Qualitative and quantitative estimation of phenolic compounds from tomato leaves showed significant accumulation of six phenolic acids, gallic (29.02 μg g−1 fresh leaf wt), ferulic (11.44 μg g−1 fresh wt), cinnamic (56.84 μg g−1 fresh wt), gentisic (24.19 μg g−1 fresh wt), chlorogenic acid (1.72 μg g−1 fresh wt) and salicylic (0.39 μg g−1 fresh wt) acid, in actinomycetes treated plants. Biochemical profiling, when correlated with plant mortality in actinomycetes treated and untreated plants, indicated that isolates vh6 and vh8 offered 44.55% and 40.14% disease reductions, respectively compared to the control. These results established that these organisms have the potential to act as biocontrol agents.

The baiting bag method was found to be useful for isolating antagonistic actinomycetes from terrestrial habitat. Out of total 110 actinomycetes isolated from rhizospheric and non-rhizospheric soil of Indo Gangetic Plains (IGP) of India, 9 isolates exhibited aggressive antagonism against Rhizoctonia solani, screened through dual culture, well diffusion and sealed plate technique. Maximum growth inhibition was recorded up to 50% under well diffusion (S. toxytricini vh22) and 52.6% in a direct confrontation (Actinomycetales bacterium vh41). Whereas maximum disease suppression (53.33%) under green house condition was achieved on seedling treated with S. tricolor vh85. Scanning electron microscopy of antagonists and pathogen interaction exhibited pore formation and hyphal degradation of test pathogen. Physiological and molecular characterization of selected isolates showed wide diversity and uncommon species has been encountered through the selective isolation technique.

Phytopathogens are one of the major entities in agro-industry, which reduces plant capacity to produce biomass and yield, resulting poor plant health. Since past few decades of the agricultural practices, various agro-chemicals and biological compositions were employed to restrict the phytopathogens, which on inappropriate application cause environmental pollution. In this context, the rapid and precise in situ detection of phytopathogens may tend specific control of phytopathogens rather the application of pesticides in non-specific manner. This ultimately prevents agroecological loss, environmental degradation and loss of biodiversity by avoiding saturation of excess agrochemicals in the agricultural lands. Among phytopathogens, Rhizoctonia solani holds potent pathogenic attributes and has a wide host range, which solely causes huge agroeconomic loss every year all over the world.

In past few decades of agriculture history, chemical fertilizers and pesticides contributed significantly to boost agro-production even in few years of introduction. Their special attributes such as quick and nonspecific action and less expensive, low-cost production and storage make them more acceptable widely. However, their lethal effects on plants, animals, humans, and the environment diverted attention toward eco-friendly alternative. In addition, developing resistance in pests becomes an unresolved puzzle in current time frame and a raising demand for reliable and environment-friendly tool for plant disease management. In view of the growing concern toward safe and nutritious food, biofertilizers and biopesticides seem crucial component of modern agriculture.