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Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine, 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.

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 effects of antibiotic treatment on antimicrobial resistance. In the first facility, sulfadiazine-trimethoprim was added prophylactically upon fingerling stocking and water column-associated Aeromonas were monitored periodically over an eleven-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 three-year period and from pond water samples to assess associations between pathogenic strains to those in the water column. A total of 1200 Aeromonas spp. were isolated, initially screened for sulfadiazine resistance and further screened against five additional antibiotics. In both facilities, strong correlations were observed between sulfadiazine resistance and trimethoprim and tetracycline resistances, whereas correlations between sulfadiazine resistance and ceftriaxone, gentamycin and chloramphenicol resistances were low. Abundance of multi-drug resistant strains as well as sul1, tetA and intI1 gene-harboring strains was 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 revealed 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.

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.