Microbial studies of compost: bacterial identification,and their potential for turfgrass pathogen suppression

Composting is the degradation of organic materials through the activities of diverse microorganisms. This research examined microbial community dynamics, population levels and identification of bacteria throughout the composting process and in storage. In addition, an evaluation was performed to determine the potential for dominant bacterial isolates to suppress selected turfgrass pathogens: Sclerotinia homoeocarpa, Pythium graminicola, Typhula ishikariensis, and Microdochium nivale, responsible for causing the turfgrass diseases dollar spot, pythium blight, typhula blight, and fusarium patch, respectively. Composts supported high population levels of bacteria with 78% of cultures tested being Gram-negative. Proteolytic activity, found in 29% of cultures tested is a potential mechanism of suppression or competition with other microorganisms. Although the Biolog system did not identify a wide range of bacteria, the main Gram-negative genera identified in mature compost were Pseudomonas (28%), Serratia (20%), Klebsiella (11%), and Enterobacter (5%). Twenty-one percent of isolates tested were not identified by Biolog, and many more had similarity indexes < 0.50. The microbial identification system, based on whole cell fatty acid analysis, identified a wide range of bacteria, with a higher proportion of similarities than the Biolog system. Genera common to both testing procedures included Pseudomonas, Serratia, and Enterobacter. All Gram-positives were identified as Bacillus spp. Phospholipid fatty acid analysis, used to estimate the diversity of microbial communities, was useful in monitoring changes in microbial population in storage and during composting, as well as estimating levels of compost maturity. Plate challenge experiments revealed a number of cultures with antagonistic activity against turfgrass pathogens. There were 52, 31, 32 and 19% of the bacterial isolates tested that exhibited antagonistic activity against S. homoeocarpa, P. graminicola, T. ishikariensis, and M. nivale, respectively. Improved understanding of microbial populations and their dynamics in composts will expand their potential to act as suppressants on pathogenic fungi or turfgrass.     

Microbial communities in wetlands of the Athabasca oil sands: genetic and metabolic characterization

Naphthenic acids are a complex family of naturally occurring cyclic and acyclic carboxylic acids that are present in the acidic fraction of petroleum. Naphthenic acids are acutely toxic to aquatic organisms. Previous studies showed that wetland sediments exposed to oil sands process water containing naphthenic acids had higher rates of naphthenic acid degradation in vitro compared with unexposed wetlands. In this study we compare the microbial community structures in sediments from wetlands exposed to different amounts of oil sands process water using BIOLOG, phospholipid fatty acid analysis and denaturing gradient gel electrophoresis of total bacterial DNA. Community profiles were compared using cluster analysis. BIOLOG profiles were primarily influenced by seasonal trends rather than naphthenic acids content. In contrast, phospholipid fatty acid analysis comparisons clustered communities that had higher levels of residual oil, although this association was not strong. In contrast, cluster diagrams produced from the denaturing gradient gel electrophoresis data clearly separated bacterial communities according to naphthenic acids concentrations, indicating that naphthenic acids content was a major influence on the composition of the bacterial community. In addition, denaturing gradient gel electrophoresis profiles indicated that naphthenic acids-exposed bacterial communities were homogeneous on a scale of meters, whereas unexposed (off-site) wetlands were less homogeneous.     

Microbial processes in the Athabasca Oil Sands and their potential applications in microbial enhanced oil recovery

The Athabasca Oil Sands are located within the Western Canadian Sedimentary Basin, which covers over 140,200 km² of land in Alberta, Canada. The oil sands provide a unique environment for bacteria as a result of the stressors of low water availability and high hydrocarbon concentrations. Understanding the mechanisms bacteria use to tolerate these stresses may aid in our understanding of how hydrocarbon degradation has occurred over geological time, and how these processes and related tolerance mechanisms may be used in biotechnology applications such as microbial enhanced oil recovery (MEOR). The majority of research has focused on microbiology processes in oil reservoirs and oilfields; as such there is a paucity of information specific to oil sands. By studying microbial processes in oil sands there is the potential to use microbes in MEOR applications. This article reviews the microbiology of the Athabasca Oil Sands and the mechanisms bacteria use to tolerate low water and high hydrocarbon availability in oil reservoirs and oilfields, and potential applications in MEOR.     

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea-land transition

Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture-dependent approach yielded a 100-isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash-zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential.     

Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure

The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies.     

Wooden art objects and the museum environment: identification and biodegradative characteristics of isolated microflora

AIMS: The identification of culturable microbial communities on wooden art objects and from indoor air, and the analysis of their biodegradative properties. METHODS AND RESULTS: Common and newly-developed agar media were used for the isolation of fungal and bacterial microflora. The identification was carried out by traditional methods and by the sequencing of 16S or 18S rDNA PCR products. Different plate assays were employed to screen the lignolytic and cellulolytic activities of the isolated microflora. Interesting bacteria were isolated from art objects even though the fungi were the principal contaminants of art works. Various fungal and bacterial species exhibited their lignolytic and cellulolytic activity by the decolorization of Remazol Brilliant Blue R, Phenol Red, Azure B and Ostazin Brilliant Red H-3B. CONCLUSIONS: The microbial communities on wooden art objects exposed in an indoor environment were identified. The study showed the biodegradative power of many microorganisms, and new data were added to this field barely investigated. SIGNIFICANCE AND IMPACT OF THE STUDY: By the development of new culture media and the evaluation of different biodegradative plate assays, a strategy for the analysis of microflora in wooden art objects was established. Several aspects of the study could be also exploited for biotechnology applications.     

Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters

[This corrects the article on p. 4101 in vol. 59.].     

Microbial communities in large-scale wood piles and their effects on wood quality and the environment

The demand of renewable energy sources, i.e. biomass, is steadily increasing worldwide to reduce the need of fossil energy sources. Biomass such as energy crops, woody species, forestry and agricultural residues are the most common renewable energy sources. Due to uneven demand for wood fuel, the material is mostly stored outdoors in chip piles or as logs until utilisation. Storage of biomass is accompanied by chemical, physical and biological processes which can significantly reduce the fuel quality. However, heating plants require high-quality biomass to ensure efficient operation, thereby minimising maintenance costs. Therefore, optimised storage conditions and duration times for chipped wood and tree logs have to be found. This paper aims at reviewing available knowledge on the pathways of microbial effects on stored woody biomass and on investigations of the fungal and bacterial community structure and identity. Moreover, potential functions of microorganisms present in wood chip piles and logs are discussed in terms of (1) reduction of fuel quality, (2) catalysing self-ignition processes, and (3) constituting health risk and unfriendly work environment.     

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments

Although bacteria are ubiquitous in the near-surface atmosphere and they can have important effects on human health, airborne bacteria have received relatively little attention and their spatial dynamics remain poorly understood. Owing to differences in meteorological conditions and the potential sources of airborne bacteria, we would expect the atmosphere over different land-use types to harbor distinct bacterial communities. To test this hypothesis, we sampled the near-surface atmosphere above three distinct land-use types (agricultural fields, suburban areas and forests) across northern Colorado, USA, sampling five sites per land-use type. Microbial abundances were stable across land-use types, with ∼10⁵–10⁶ bacterial cells per m³ of air, but the concentrations of biological ice nuclei, determined using a droplet freezing assay, were on average two and eight times higher in samples from agricultural areas than in the other two land-use types. Likewise, the composition of the airborne bacterial communities, assessed via bar-coded pyrosequencing, was significantly related to land-use type and these differences were likely driven by shifts in the sources of bacteria to the atmosphere across the land-uses, not local meteorological conditions. A meta-analysis of previously published data shows that atmospheric bacterial communities differ from those in potential source environments (leaf surfaces and soils), and we demonstrate that we may be able to use this information to determine the relative inputs of bacteria from these source environments to the atmosphere. This work furthers our understanding of bacterial diversity in the atmosphere, the terrestrial controls on this diversity and potential approaches for source tracking of airborne bacteria.     

Edge-count probabilities for the identification of local protein communities and their organization

We present a computational approach based on a local search strategy that discovers sets of proteins that preferentially interact with each other. Such sets are referred to as protein communities and are likely to represent functional modules. Preferential interaction between module members is quantified via an analytical framework based on a network null model known as the random graph with given expected degrees. Based on this framework, the concept of local protein community is generalized to that of community of communities. Protein communities and higher-level structures are extracted from two yeast protein interaction data sets and a network of published interactions between human proteins. The high level structures obtained with the human network correspond to broad biological concepts such as signal transduction, regulation of gene expression, and intercellular communication. Many of the obtained human communities are enriched, in a statistically significant way, for proteins having no clear orthologs in lower organisms. This indicates that the extracted modules are quite coherent in terms of function.     

Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach

The advent of whole-genome sequencing of bacteria and advances in bioinformatics have revolutionized the study of bacterial pathogenesis, enabling the targeting of possible vaccine candidates starting from genomic information. Nowadays, the availability of hundreds of bacterial genomes enables identification of the genetic differences across several genomes from the same species. The unexpected degree of intra-species diversity suggests that a single genome sequence is not entirely representative and does not offer a complete picture of the genetic variability of a species. The practical consequence is that, in many cases, a universal vaccine is possible only by including a combination of antigens and this combination must take into account the pathogen population structure.     

A study on the microbiota from olive-mill wastewater (OMW) disposal lagoons, with emphasis on filamentous fungi and their biodegradative potential

The microbial composition of olive mill wastewater (OMW) from four disposal ponds has been studied. Such OMW samples contained a variable (but high) number of bacteria, yeasts and molds. Among the latest, members of twelve different genera (Acremonium, Alternaria, Aspergillus, Chalara, Fusarium, Lecytophora, Paecilomyces, Penicillium, Phoma, Phycomyces, Rhinocladiella and Scopulariopsis) were found. Members of five genera (Chalara, Fusarium, Paecilomyces, Penicillium and Scopulariopsis) were widely distributed, and they were able to grow efficiently in undiluted OMW as a sole source of nutrients. Strains of Fusarium, Paecilomyces, Penicillium and Scopulariopsis showed a marked capacity for OMW detoxification, depleting its antibacterial activity almost completely.     

Microbial communities in the saturated groundwater environment II: Diversity of bacterial communities in a Pleistocene sand aquifer and their in vitro activities

Bacterial cell numbers obtained from 103 water and sediment samples from a Pleistocene sandy aquifer in the Lower Rhine region (Bocholt, FRG) were determinated on P-agar and by direct count. Below 5 m under the surface, colony-forming unit (cfu) numbers in water samples were less than 100/ml, and in many cases less than 50/ml. In sediment samples, they were 10- to 100-fold higher (10²–10⁴ cfu/g dry wt), but changing markedly between different depths. Direct cell counts yielded numbers two to three orders of magnitude higher.About 2,700 strains of bacteria from 60 samples were isolated randomly and characterized by morphological and physiological properties. Of all the isolates, 71.6% were gram-negative, and 52.2% were gram-negative straight rods. Water communities, with one exception, had low proportions of gram-positive bacteria (<11%), whereas in all but one of the sediment communities percentages of gram-positive isolates were three- to sevenfold higher (35–43%). Water and sediment communities, as well as communities from different sampling sites and communities from different depths of the same sampling site, differed in their qualitative and quantitative morphotype composition and physiological capabilities.The in vitro activities of strains within a single community were quite different, indicating that each community is composed of many diverse bacteria, several having extremely different capabilities. Thus, each community has its own specific activity pattern. Gram-positive bacteria showed on an average lower total activities than did gram-negative bacteria. Grampositive bacteria as well as gram-negative bacteria from sediment had higher values of in vitro activities than the corresponding groups isolated from water. Many water and sediment bacteria preferred the same substrates which were utilized at high rates. However, there were differences in the degradation of the various other substrates present, and each community showed preferences for particular substrates, which they degraded best.The results of cell morphology and physiology studies indicated that all eight characterized communities were very different from one another and very diversely structured.     

The impact of wildfire on vesicular-arbuscular mycorrhizal fungi and their potential to influence the re-establishment of post-fire plant communities

Wildfires are a typical event in many Australian plant communities. Vesicular-arbuscular mycorrhizal (VAM) fungi are important for plant growth in many communities, especially on infertile soils, yet few studies have examined the impact of wildfire on the infectivity of VAM fungi. This study took the opportunity offered by a wildfire to compare the infectivity and abundance of spores of VAM fungi from: (i) pre-fire and post-fire sites, and (ii) post-fire burned and unburned sites. Pre-fire samples had been taken in May 1990 and mid-December 1990 as part of another study. A wildfire of moderate intensity burned the site in late December 1990. Post-fire samples were taken from burned and unburned areas immediately after the fire and 6 months after the fire. A bioassay was used to examine the infectivity of VAM fungi. The post-fire soil produced significantly less VAM infection than the pre-fire soil. However, no difference was observed between colonization of plant roots by VAM fungi in soil taken from post-fire burned and adjacent unburned plots. Soil samples taken 6 months after the fire produced significantly more VAM than corresponding soil samples taken one year earlier. Spore numbers were quantified be wet-sieving and decanting of 100-g, air-dried soil subsamples and microscopic examination. For the most abundant spore type, spore numbers were significantly lower immediately post-fire. However, no significant difference in spore numbers was observed between post-fire burned and unburned plots. Six months after the fire, spore numbers were the same as the corresponding samples taken 1 year earlier. All plants appearing in the burned site resprouted from underground organs. All post-fire plant species recorded to have mycorrhizal associations before the fire had the same associations after the fire, except for species of Conospermum (Proteaceae), which lacked internal vesicles in cortical cells in the post-fire samples.     

Crop seed oil bodies: From challenges in protein identification to an emerging picture of the oil body proteome

Oleaginous seeds store lipids in specialized structures called oil bodies (OBs). These organelles consist of a core of neutral lipids bound by proteins embedded in a phospholipid monolayer. OB proteins are well conserved in plants and have long been grouped into only two categories: structural proteins or enzymes. Recent work, however, which identified other classes of proteins associated with OBs, clearly shows that this classification is obsolete. Proteomics‐mediated OB protein identification is facilitated in plants for which the genome is sequenced and annotated. However, it is not clear whether this knowledge can be dependably transposed to less well‐characterized plants, including the well‐established commercial sources of seed oil as well as the many others being proposed as novel sources for biodiesel, especially in Africa and Asia. Toward an update of the current data available on OB proteins this review discusses (i) the specific difficulties for proteomic studies of organelles; (ii) a 2012 census of the proteins found in seed OBs from various crops; (iii) the oleosin composition of OBs and their role in organelle stability; (iv) PTM of OB proteins as an emerging field of investigation; and finally we describe the emerging model of the OB proteome from oilseed crops.     

Microbial communities in a porphyry copper tailings impoundment and their impact on the geochemical dynamics of the mine waste

The distribution and diversity of acidophilic bacteria of a tailings impoundment at the La Andina copper mine, Chile, was examined. The tailings have low sulfide (1.7% pyrite equivalent) and carbonate (1.4% calcite equivalent) contents and are stratified into three distinct zones: a surface (0-70-80 cm) 'oxidation zone' characterized by low-pH (2.5-4), a 'neutralization zone' (70-80 to 300-400 cm) and an unaltered 'primary zone' below 400 cm. A combined cultivation-dependent and biomolecular approach (terminal restriction enzyme fragment length polymorphism and 16S rRNA clone library analysis) was used to characterize the indigenous prokaryotic communities in the mine tailings. Total cell counts showed that the microbial biomass was greatest in the top 125 cm of the tailings. The largest numbers of bacteria (10(9) g(-1) dry weight of tailings) were found at the oxidation front (the junction between the oxidation and neutralization zones), where sulfide minerals and oxygen were both present. The dominant iron-/sulfur-oxidizing bacteria identified at the oxidation front included bacteria of the genus Leptospirillum (detected by molecular methods), and Gram-positive iron-oxidizing acidophiles related to Sulfobacillus (identified both by molecular and cultivation methods). Acidithiobacillus ferrooxidans was also detected, albeit in relatively small numbers. Heterotrophic acidophiles related to Acidobacterium capsulatum were found by molecular methods, while another Acidobacterium-like bacterium and an Acidiphilium sp. were isolated from oxidation zone samples. A conceptual model was developed, based on microbiological and geochemical data derived from the tailings, to account for the biogeochemical evolution of the Piuquenes tailings impoundment.     

Psilostachyin, acetylated pseudoguaianolides and their analogues: preparation and evaluation of their anti-inflammatory potential

Naturally occurring acetylated pseudoguaianolides and psilostachyin including their analogues were synthesized. The structure of semi-synthetic psilostachyin was also confirmed by X-ray crystallography. The anti-inflammatory potential of all the derivatives has been evaluated through in vitro expression of TNF-α, IL-1β and IL-6 in murine neutrophils.     

Bryophyte communities of Mediterranean Europe: a first approach to model their potential distribution in highly seasonal rivers

Mediterranean watercourses are among the most threatened ecosystems worldwide, being increasingly important to understand environmental drivers of biotic assemblages. Our aim was to provide a comprehensive picture of bryophyte communities in Mediterranean rivers and to determine the environmental factors that influence their distribution. We used floristic data collected for inter-calibration purposes under the European Water Framework Directive and River Habitat Survey, from 474 river reaches in six countries of the European Mediterranean basin. We analysed data through classification, ordination and environmental niche modelling techniques, and classified taxa according to biogeographic and aquatic habitat frameworks developed specifically for bryophytes. These analyses revealed four types of communities influenced by spatio-temporal precipitation patterns, altitude and water chemistry factors, most notably calcium and manganese. Community types are compositionally differentiated, although they share some core taxa and show an overall tendency to have several temperate and exclusively aquatic taxa despite the intermittent nature of water flow in highly seasonal Mediterranean rivers. The modelling approach can be improved at a more local scale when more bryological data and higher-resolution environmental information become available. Given future scenarios of climate change and human alteration of hydrological regimes, broader scales studies are needed to monitor shifts in bryophyte communities.