Microbial diversity

An innovative bioprocess method, Systematic Environmental Molecular Bioremediation Technology (SEMBT) that combines bioaugmentation and biostimulation with a molecular monitoring microarray biochip, was developed as an integrated bioremediation technology to treat S-and ...

The description of microbial diversity by molecular culture-independent techniques most often involves the amplification of the 16S rRNA by PCR gene and either analysis of the diversity of amplified molecules (community fingerprinting) that allows the simultaneous study of many samples or the cloning and sequencing of a significant amount of amplification products. The fact that between the 16S and the 23S genes in the ribosomal operon there is a spacer extremely variable in both sequence and length provides an excellent tool to simplify both approaches. The spacer can be amplified almost as easily as the 16S rDNA taking advantage of conserved nucleotide stretches at the 5' end of the 23S gene and the amplicon can contain different amounts of the 16S rDNA choosing primers at the different conserved areas within this gene. Identified by the acronym RISA (rDNA internal spacer analysis), the spacer addition provides a marker of highly variable size allowing standard separation of the amplification products and the sequence of this hypervariable region is useful in the fine discrimination of operational taxonomic units.

Rice fields represent “hot spots of biodiversity” – encompassing a complicated network of aerobic, anaerobic and facultative micro-organisms, whose interactions with the resident macro flora and fauna lead to unique and complex biochemical and physicochemical reactions. In turn, these reactions fuel the major nutrient cycles. The dynamics of microbiological activity of rice soil, especially in the rhizosphere, represents a model system to study the fundamentals of microbial ecology, such as the mechanisms for maintenance and communication between diverse and overlapping bacterial populations. Modern molecular tools such as innovative micro-scale-measuring devices and use of extensive long-term field data have revealed the culturable/unculturable diversity – which includes not only the commonly recorded eubacteria and cyanobacteria but also members of Archaea, Planctomycetes, β-Proteobacteria, and an increasing number of associated endophytes. This compilation presents the current knowledge about this key soil habitat and its global significance to agriculture and the environment.

Pesticides are extensively used in agriculture as a part of pest control strategies. Owing to their xenobiotics characteristics, pesticides may adversely affect the proliferation of beneficial soil microorganisms and their associated biotransformation in the soil. Inactivation of nitrogen‐fixing and phosphorus‐solubilizing microorganisms is observed in pesticide‐contaminated soils. Recent studies show that some pesticides disturb molecular interactions between plants and N‐fixing rhizobacteria

The sustainability of rice production systems globally is intricately related to the chemistry, physics and biology of rice soils – with basic properties differing considerably in wet/dry land soils, tropical/temperate areas or even with the soil surface or rhizosphere niche of the field. Rice fields represent unique aqua-terrestrial ecosystems in which the tremendous diversity of soil microbes, soil fauna and plants – ranging in function from nitrogen fixers, nitrifiers, methanogens, methane oxidizers, phosphate-dissolving microbes, sulfur oxidizers to catabolizers of pesticides is observed. This diversity is inclusive of bacteria, cyanobacteria, archaea, planctomycetes and β-proteobacteria, besides the increasing members of endophytes associated. The complexity and dynamic nature of this ecosystem requires in-depth investigations of the tripartite interactions among plants, microbes and the soil–water environment. This needs to be complemented with studies on the ecological compartmentalization due to diffusion gradients of nutrients and gases, which is of extreme significance in the current scenario of problems associated with greenhouse gas emissions from agricultural areas, especially rice paddies. This article provides an overview of the interactions between the microflora and crop, with emphasis on nutrient transformations in the rhizosphere, so as to develop effective and efficient environmentally sustainable strategies for this crop.

With the increasing successful stories of decontamination, different strategies for metal remediation are gaining importance and popularization in developing countries. Rhizoremediation, is one such promising option that harnesses the impressive capabilities of microorganisms associated with roots to degrade organic pollutants and transform toxic metals. Since it is a plant based in-situ phytorestoration technique it is proven to be economical, efficient and easy to implement under field conditions. Plants grown in metal contaminated sites harbor unique metal tolerant and resistant microbial communities in their rhizosphere. These rhizo-microflora secrete plant growth promoting substances, siderophores, phytochelators to alleviate metal toxicity, enhance the bioavailability of metals (phytoremediation) and complexation of metals (phytostabilisation). Selection of right bacteria/consortia and inoculation to seed/ roots of suitable plant species will widen the perspectives of rhizoremediation.

The use of treatment wetlands (TWs) in the treatment of domestic, municipal and industrial wastewater has been well-documented in past years. Although there are a number of different mechanisms at play in the removal of pollutants in these wetlands, it has been shown that one of the most significant means of wastewater polishing is due to the contribution of microbial communities (Cui et al., 2013; Wu et al., 2012). Microorganisms that occur naturally in wetland environments have the ability to degrade organic compounds and metabolize contaminants, effectively contributing to the transformation and removal of key wastewater parameters such as nitrogen, ammonia, biochemical/chemical oxygen demand (BOD/COD), phosphorus and heavy metals (Faulwetter et al., 2009; Saeed & Sun, 2013). As well, the ability of microorganisms to aggregate together and form unique biofilms creates an even more potent method of wastewater treatment, contributing to pollutant removal by the indirect impact on hydrological parameters and interactions with the rhizosphere (Gagnon & Weber, 2014).
Although the specific metabolic processes contributing to wastewater treatment are relatively well understood, the characterization and community structure of microorganisms in TWs are not, and there has been little research conducted on the engineering of wetlands aimed at enhancing microbial activity or specific bacterial processes. In recent years, however, techniques for assessing the function, enumeration, diversity and distribution of microorganisms in treatment wetlands have become increasingly sophisticated, leading to the emergence of more and more studies attempting to identify and control the specific factors influencing microorganisms (Gagnon & Weber, 2014). This paper begins with a summary of the main microbial functions and processes leading to contaminant reduction. It then moves on to outline some of the wetland characteristics that have proven to influence these processes as well as the density, activity and/or structural community of microorganisms. In addition, suggestions will be made throughout this paper about the ability to attenuate microbial treatment by making alterations to these variable wetland characteristics.

The recent geomicrobiological characterization of Río Tinto, Iberian Pyrite Belt (IPB), has proven the importance of the iron cycle, not only in generating the extreme conditions of the habitat (low pH, high concentration of toxic heavy metals) but also in maintaining the high level of microbial diversity, both prokaryotic and eukaryotic, detected in the water column and the sediments. The extreme conditions of the Tinto basin are not the product of industrial contamination but the consequence of the presence of an underground bioreactor that obtains its energy from the massive sulfide minerals of the IPB. To test this hypothesis, a drilling project was carried out to intersect ground waters that interact with the mineral ore in order to provide evidence of subsurface microbial activities and the potential resources to support these activities. The oxidants that drive the system appear to come from the rock matrix, contradicting conventional acid mine drainage models. These resource...

The development of techniques in molecular biology has led to their application to microbial ecology. The extraction of DNA, followed by the use of Polymerase Chain Reaction (PCR) to amplify a gene common to all organisms can provide information about microbial community structure, microbial diversity, evolution and taxonomy. Two methods, namely SDS-based extraction method and FastPrepTM method, were evaluated using four different soil samples represent major types of Egyptian soils. The DNA fragment size in the extracts from all soils was >23 kb. The DNA yield from the 4 soils ranged from 18 -52 µg of DNA g-1. The highest DNA yield was observed in Beni-Suef soil rich in organic carbon and nitrogen content and high microbial population. However, Ismalia soil, which is low in organic carbon, nitrogen content and microbial population, had the lowest DNA yield. DNA extracts by SDS based method from all soils did not exhibit high absorbance ratios, due to the presence of absorbing co...

Actively forming gypsum deposits at the Guerrero Negro sabkha and saltern system provided habitats for stratified, pigmented microbial communities that exhibited significant morphological and phylogenetic diversity. These deposits ranged from meter-thick gypsum crusts forming in saltern seawater concentration ponds to columnar microbial mats with internally crystallized gypsum granules developing in natural anchialine pools. Gypsum-depositing environments were categorized as forming precipitation surfaces, biofilm-supported surfaces, and clastic surfaces. Each surface type was described in terms of depositional environment, microbial diversity, mineralogy, and sedimentary fabrics. Precipitation surfaces developed in high-salinity subaqueous environments where rates of precipitation outpaced the accumulation of clastic, organic, and/or biofilm layers. These surfaces hosted endolithic biofilms comprised predominantly of oxygenic and anoxygenic phototrophs, sulfate-reducing bacteria, and bacteria from the phylum Bacteroidetes. Biofilm-supported deposits developed in lower-salinity subaqueous environments where light and low water-column turbulence supported dense benthic microbial communities comprised mainly of oxygenic phototrophs. In these settings, gypsum granules precipitated in the extracellular polymeric substance (EPS) matrix as individual granules exhibiting distinctive morphologies. Clastic surfaces developed in sabkha mudflats that included gypsum, carbonate, and siliclastic particles with thin gypsum/biofilm components. Clastic surfaces were influenced by subsurface brine sheets and capillary evaporation and precipitated subsedimentary gypsum discs in deeper regions. Biofilms appeared to influence both chemical and physical sedimentary processes in the various subaqueous and subaerially exposed environments studied. Biofilm interaction with chemical sedimentary processes included dissolution and granularization of precipitation surfaces, formation of gypsum crystals with equant and distorted habits, and precipitation of trace carbonate and oxide phases. Fine-scale wrinkle structures visible in clastic surfaces of sabkha environments offered evidence of the biofilm's role in physical sedimentary processes. These findings are highly relevant to astrobiology because they expand and refine the known characteristics of gypsum deposits, including their biological components.