Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype–dependent finetuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth–promoting and plant health–promoting bacteria.

Structure and functions of the bacterial microbiota of plants

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

Our knowledge of the microbiology of the phyllosphere, or the aerial parts of plants, has historically lagged behind our knowledge of the microbiology of the rhizosphere, or the below-ground habitat of plants, particularly with respect to fundamental questions such as which microorganisms are present and what they do there. In recent years, however, this has begun to change. Cultivation-independent studies have revealed that a few bacterial phyla predominate in the phyllosphere of different plants and that plant factors are involved in shaping these phyllosphere communities, which feature specific adaptations and exhibit multipartite relationships both with host plants and among community members. Insights into the underlying structural principles of indigenous microbial phyllosphere populations will help us to develop a deeper understanding of the phyllosphere microbiota and will have applications in the promotion of plant growth and plant protection.

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Microbial life in the phyllosphere

Among different conversion processes for biomass, biological anaerobic digestion is one of the most economic ways to produce biogas from various biomass substrates In addition to hydrolysis of polymeric substances, the activity and performance of the methanogenic bacteria is of paramount importance during methanogenesis The aim of this paper is primarily to review the recent literature about the occurrence of both acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of particulate biomass to methane (not wastewater treatment), while this review does not cover the activity of the acetate oxidizing bacteria Both acetotrophic and hydrogenotrophic methanogens are essential for the last step of methanogenesis, but the reports about their roles during this phase of the process are very limited Despite, some conclusions can still be drawn At low concentrations of acetate, normally filamentous Methanosaeta species dominate, eg, often observed in sewage sludge Apparently, high concentrations of toxic ionic agents, like ammonia, hydrogen sulfide (H2S) and volatile fatty acids (VFA), inhibit preferably Methanosaetaceae and especially allow the growth of Methanosarcina species consisting of irregular cell clumps, eg, in cattle manure Thermophilic conditions can favour rod like or coccoid hydrogenotrophic methanogens Thermophilic Methanosarcina species were also observed, but not thermophilic Methanosaetae Other environmental factors could favour hydrogentrophic bacteria, eg, short or low retention times in a biomass reactor However, no general rules regarding process parameters could be derivated at the moment, which favours hydrogenotrophic methanogens Presumably, it depends only on the hydrogen concentration, which is generally not mentioned in the literature

The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review

Prior to the work of Cable and Hopp (J. Parasit. 40(6): 674.680, 1954) Neoechinorhynchus emydis (L e i d y, 1851) was the only recognized species of Acanthocephala in North American turtles. To date, a total of five species have been described. Of these, two species (Neoechinorbynchus pseudemydis Cable and Hopp, 1954, and N. emyditoides Fisher, 1960) were recovered from six of 12 Louisiana turtles (Pseudemys scripta elegans (Wied)) examined by Fisher (J. Parasit. 46(2): 257-266, 1960). He (1960) also found N. chrysemydis Cable and Hopp, 1954 in Pseudemys scripta subsp. The data pt .sented are results of studies conducted between the spring of 1965 and the summer of 1966. Seventynine turtles (48 female and 31 males) encompassing seven species (47 Pseudemys scripta elegans (Wied), three P. floridana hoyi (Holbrook), eight Chelydra serpentina serpentina (L.), eight Kinosternon subrubrum hippocrepis Gray, seven Terrapene carolina carolina (L.), five T. c. triunguis (Agassiz) and one Trionyx muticus (LeSueur) collected from Baton Rouge and vicinity were examined. This investigation revealed the presence of three species of Acanthocephala (Neoechinorhynchus pseudemydis, N. emyditoides, and N. chrysemydis) in Louisiana turtles and confirms Fisher’s (1960) work. Of the seven species of turtles examined, only P. s. e!egans (25 16 females and 9 males) and P. floridana hoyi (2 females) were positive with infection. Three of the 25 P. s. e!egans had mixed infection comprising three species of Neoechinorhynchus while seven had two species respectively. P. f!oridana hoyi represents a host record for N. chrysemydis;

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Myiasis in man and animals in the old world

Coastal lagoons are represented by steep gradients in physical, chemical, and biological parameters and are regarded as one of the most productive ecosystems in the world. These lagoons are at an intermediate position between the freshwater and marine water systems. Huge amount of influx of organic matter and nutrient load with the freshwater inputs can be seen in such lagoons. The increased influx of organic matter and nutrients fuel in the lagoon increases the chance of eutrophication. The sedimentary microbial communities play an important role in preventing eutrophication by supporting a diverse assemblage of aerobic and anaerobic microbial communities. Considering the importance of sedimentary bacterial communities, numerous studies have investigated their ecological roles and biogeographical patterns in a variety of aquatic ecosystems. Compared to the marine and freshwater ecosystems, estuarine coastal lagoons are highly dynamic, still are poorly understood with respect to their sedimentary communities. Our hypothesis was that bacterial communities would exhibit biogeographical patterns which would be strongly associated with the biotic and abiotic factors. Using Illumina sequencing of the 16S rRNA genes from bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of an exotic weed; P. karka and a native seagrass species; H. uninervis in a brackish water estuarine lagoon, Chilika (India). Comparison of bacterial communities with the environmental factor was done using Redundancy analysis. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities in a tropical brackish water coastal lagoon and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities. Citation: Behera, P., Mahapatra, S., Mohapatra, M., Kim, J.Y., Adhya, T.K., Raina, V., Suar, M., Pattnaik, A.K. and Rastogi, G. Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water coastal lagoon [Abstract]. In: Abstracts of the NGBT conference; Oct 02-04, 2017; Bhubaneswar, Odisha, India: Can J biotech, Volume 1, Special Issue, Page 133. https://doi.org/10.24870/cjb.2017-a119

http://www.canadianjbiotech.com/CAN_J_BIOTECH/Archives/v1/Special Issue/cjb.2017-a119.pdf

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water coastal lagoon

Cyanobacteria play an important role in primary production and nitrogen fixation. Although Cyanobacteria are well-known diazotrophic organisms, their role in other steps Nitrogen Cycle is obscure. Screening of Cyanobacterial genomes from cultured and unculturable species can help identify potentially novel functions. In this study, we assembled Cyanobacterial genomes from metagenomic data generated from environmental DNA isolated from a brackish water lagoon (Chilika, India). We annotated these Cyanobacterial metagenome-assembled genomes (MAG) for all the encoded functions using KEGG Orthology. We found two high-quality Cyanobacterial MAGs containing the nirBD gene and nifH and nifD genes involved in the nitrogen cycle. nirBD encodes for the Dissimilatory Nitrate Reduction to Ammonium (DNRA) activity, a function previously not ascribed to Cyanobacteria. We validated the presence of NirBD in publicly available isolate genomes of Cyanobacteria and examined its evolution in the phylum by phylogenetic reconciliation of species and gene trees. Our analysis revealed that both horizontal gene transfers and speciation events contributed to the dispersal of the nirBD gene in Cyanobacteria. We observed that mostly filamentous Cyanobacteria served as ancestral donors in horizontal gene transfer events. Further, we found that the nirBD gene is under a purifying selection pressure in Cyanobacteria. This study demonstrates the genomic potential and evolution of DNRA activity in Cyanobacteria for the utilisation of nitrate in the ecosystem which can help these organisms to cope with extreme environmental conditions. It expands our overall comprehension of the contribution of Cyanobacteria in the biogeochemical cycling in aquatic ecosystems.

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Genomic potential and evolution of Dissimilatory Nitrate Reduction to Ammonium in Cyanobacteria

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon.

Gurdeep Rastogi

Papers

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water coastal lagoon

Genomic potential and evolution of Dissimilatory Nitrate Reduction to Ammonium in Cyanobacteria

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon.

Seagrasses and local environment control the bacterial community structure and carbon substrate utilization in brackish sediments.

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