Gurdeep Rastogi

Bio: Gurdeep Rastogi is an academic researcher from South Dakota School of Mines and Technology. The author has contributed to research in topics: Brackish water & Phytoplankton. The author has an hindex of 22, co-authored 60 publications receiving 2240 citations. Previous affiliations of Gurdeep Rastogi include University of California, Davis & University of California.

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce.

Abstract: The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009-2010 crop cycle. Total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial 'core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.

Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment

Abstract: Culture-based methods are important in investigating the microbial ecology of natural and anthropogenically impacted environments, but they are extremely biased in their evaluation of microbial genetic diversity by selecting a particular population of microorganisms. With recent advances in genomics and sequencing technologies, microbial community analyses using culture-independent molecular techniques have initiated a new era of microbial ecology. Molecular analyses of environmental communities have revealed that the cultivable fraction represents <1% of the total number of prokaryotic species present in any given sample. A variety of molecular methods based on direct isolation and analysis of nucleic acids, proteins, and lipids from environmental samples have been discovered and revealed structural and functional information about microbial communities. Molecular approaches such as genetic fingerprinting, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics are vital for discovering and characterizing the vast microbial diversity and understanding their interactions with biotic and abiotic environmental factors. This chapter summarizes recent progress in the area of molecular microbial ecology with an emphasis on novel techniques and approaches that offer new insights into the phylogenetic and functional diversity of microbial assemblages. The advantages and pitfalls of commonly used molecular methods to investigate microbial communities are discussed. The potential applications of each molecular technique and how they can be combined for a greater comprehensive assessment of microbial diversity has been illustrated with example studies.

New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches.

Abstract: The phyllosphere is an ecologically and economically important ecosystem that hosts a large and diverse microbial community. Phyllosphere microbiota play a critical role in protecting plants from diseases as well as promoting their growth by various mechanisms. There are serious gaps in our understanding of how and why microbiota composition varies across spatial and temporal scales, the ecology of leaf surface colonizers and their interactions with their host, and the genetic adaptations that enable phyllosphere survival of microorganisms. These gaps are due in large part to past technical limitations, as earlier studies were restricted to the study of culturable bacteria only and used low-throughput molecular techniques to describe community structure and function. The availability of high-throughput and cost-effective molecular technologies is changing the field of phyllosphere microbiology, enabling researchers to begin to address the dynamics and composition of the phyllosphere microbiota across a large number of samples with high, in-depth coverage. Here, we discuss and connect the most recent studies that have used next-generation molecular techniques such as metagenomics, proteogenomics, genome sequencing, and transcriptomics to gain new insights into the structure and function of phyllosphere microbiota and highlight important challenges for future research.

Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA.

Abstract: The present study investigated the cultivable mesophilic (37°C) and thermophilic (60°C) cellulose-degrading bacterial diversity in a weathered soil-like sample collected from the deep subsurface (1.5 km depth) of the Homestake gold mine in Lead, South Dakota, USA. Chemical characterization of the sample by X-ray fluorescence spectroscopy revealed a high amount of toxic heavy metals such as Cu, Cr, Pb, Ni, and Zn. Molecular community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from enrichment cultures growing in presence of microcrystalline cellulose as the sole source of carbon. All phylotypes retrieved from enrichment cultures were affiliated to Firmicutes. Cellulose-degrading mesophilic and thermophilic pure cultures belonging to the genera Brevibacillus, Paenibacillus, Bacillus, and Geobacillus were isolated from enrichment cultures, and selected cultures were studied for enzyme activities. For a mesophilic isolate (DUSELG12), the optimum pH and temperature for carboxymethyl cellulase (CMCase) were 5.5 and 55°C, while for a thermophilic isolate (DUSELR7) they were 5.0 and 75°C, respectively. Furthermore, DUSELG12 retained about 40% CMCase activity after incubation at 60°C for 8 h. Most remarkably, thermophilic isolate, DUSELR7 retained 26% CMCase activity at 60°C up to a period of 300 h. Overall, the present work revealed the presence of different cellulose-degrading bacterial lineages in the unique deep subsurface environment of the mine. The results also have strong implications for biological conversion of cellulosic agricultural and forestry wastes to commodity chemicals including sugars.

Structure and functions of the bacterial microbiota of plants

Abstract: 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.

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

Abstract: 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.

Microbial life in the phyllosphere

Abstract: 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.

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

Abstract: 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

Myiasis in man and animals in the old world

Abstract: 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;