Microbial Communities in Pre-Columbian Coprolites

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures.     

MicroRNA Expression Profiling in Mild Asthmatic Human Airways and Effect of Corticosteroid Therapy

Background

Asthma is a common disease characterised by reversible airflow obstruction, bronchial hyperresponsiveness and chronic inflammation, which is commonly treated using corticosteroids such as budesonide. MicroRNAs (miRNAs) are a recently identified family of non-protein encoding genes that regulate protein translation by a mechanism entitled RNA interference. Previous studies have shown lung-specific miRNA expression profiles, although their importance in regulating gene expression is unresolved. We determined whether miRNA expression was differentially expressed in mild asthma and the effect of corticosteroid treatment.

Methodology/Principal Findings

We have examined changes in miRNA using a highly sensitive RT-PCR based approach to measure the expression of 227 miRNAs in airway biopsies obtained from normal and mild asthmatic patients. We have also determined whether the anti-inflammatory action of corticosteroids are mediated through miRNAs by determining the profile of miRNA expression in mild asthmatics, before and following 1 month twice daily treatment with inhaled budesonide. Furthermore, we have analysed the expression of miRNAs from individual cell populations from the airway and lung.We found no significant difference in the expression of 227 miRNAs in the airway biopsies obtained from normal and mild asthmatic patients. In addition, despite improved lung function, we found no significant difference in the miRNA expression following one month treatment with the corticosteroid, budesonide. However, analysis of bronchial and alveolar epithelial cells, airway smooth muscle cells, alveolar macrophages and lung fibroblasts demonstrate a miRNA expression profile that is specific to individual cell types and demonstrates the complex cellular heterogeneity within whole tissue samples.

Conclusions

Changes in miRNA expression do not appear to be involved in the development of a mild asthmatic phenotype or in the anti-inflammatory action of the corticosteroid budesonide.     

The Expression and Activity of Cathepsins D,H and K in Asthmatic Airways

Tumstatin is an anti-angiogenic collagen IV α3 fragment, levels of which are reduced in the airways of asthmatics. Its reduction may be due to the degradation by extracellular matrix (ECM) proteases. Cathepsins play a role in ECM remodelling, with cathepsin D, H and K (CTSD, CTSH and CTSK) being associated with lung diseases. CTSD modulates the NC1 domains of collagen molecules including tumstatin, while CTSH and CTSK are involved in ECM degradation. The role of these cathepsins in the regulation of tumstatin in the lung has not previously been examined. We demonstrated that CTSB, D, F, H, K, L and S mRNA was expressed in the airways. Quantification of immunohistochemistry showed that there is no difference in the global expression of CTSD, CTSH and CTSK between asthmatics and non-asthmatics. CTSD and CTSK, but not CTSH had the capacity to degrade tumstatin. No difference was observed in the activity of CTSD and H in bronchoalveolar lavage fluid of asthmatic and non-asthmatics, while CTSK was undetectable. This indicates that while CTSD possesses the potential to directly regulate tumstatin, and thus angiogenesis through this mechanism however, it is not likely to be involved in the dysregulation of tumstatin found in asthmatic airways.     

Microbial Communities as Experimental Units

Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis.     

Defining Division of Labor in Microbial Communities

In order to survive and reproduce, organisms must perform a multitude of tasks. However, trade-offs limit their ability to allocate energy and resources to all of these different processes. One strategy to solve this problem is to specialize in some traits and team up with other organisms that can help by providing additional, complementary functions. By reciprocally exchanging metabolites and/or services in this way, both parties benefit from the interaction. This phenomenon, which has been termed functional specialization or division of labor, is very common in nature and exists on all levels of biological organization. Also, microorganisms have evolved different types of synergistic interactions. However, very often, it remains unclear whether or not a given example represents a true case of division of labor. Here we aim at filling this gap by providing a list of criteria that clearly define division of labor in microbial communities. Furthermore, we propose a set of diagnostic experiments to verify whether a given interaction fulfills these conditions. In contrast to the common use of the term, our analysis reveals that both intraspecific and interspecific interactions meet the criteria defining division of labor. Moreover, our analysis identified non-cooperators of intraspecific public goods interactions as growth specialists that divide labor with conspecific producers, rather than being social parasites. By providing a conceptual toolkit, our work will help to unambiguously identify cases of division of labor and stimulate more detailed investigations of this important and widespread type of inter-microbial interaction.     

Urea Transformation of Wetland Microbial Communities

Transformation of urea to ammonium is an important link in the nitrogen cycle in soil and water. Although microbial nitrogen transformations, such as nitrification and denitrification, are well studied in freshwater sediment and epiphytic biofilm in shallow waters, information about urea transformation in these environments is scarce. In this study, urea transformation of sedimentary, planktonic, and epiphytic microbial communities was quantified and urea transformation of epiphytic biofilms associated with three different common wetland macrophyte species is compared. The microbial communities were collected from a constructed wetland in October 2002 and urea transformation was quantified in the laboratory at in situ temperature (12°C) with the use of the ¹⁴C-urea tracer method, which measures the release of ¹⁴CO₂ as a direct result of urease activity. It was found that the urea transformation was 100 times higher in sediment (12–22 mmol urea-N m⁻² day⁻¹) compared with the epiphytic activity on the surfaces of the submerged plant Elodea canadensis (0.1–0.2 mmol urea-N m⁻² day⁻¹). The epiphytic activity of leaves of Typha latifolia was lower (0.001–0.03 mmol urea-N m⁻² day⁻¹), while urea transformation was negligible in the water column and on the submerged leaves of the emergent plant Phragmites australis. However, because this wetland was dominated by dense beds of the submerged macrophyte E. canadensis, this plant provided a large surface area for epiphytic microbial activity—in the range of 23–33 m² of plant surfaces per square meter of wetland. Thus, in the wetland system scale at the existing plant distribution and density, the submerged plant community had the potential to transform 2–7 mmol urea-N m⁻² day⁻¹ and was in the same magnitude as the urea transformation in the sediment.     

Mineral Type Structures Soil Microbial Communities

Soil microorganisms living in close contact with minerals play key roles in the biogeochemical cycling of elements, soil formation, and plant nutrition. Yet, the composition of microbial communities inhabiting the mineralosphere (i.e., the soil surrounding minerals) is poorly understood. Here, we explored the composition of soil microbial communities associated with different types of minerals in various soil horizons. To this effect, a field experiment was set up in which mineral specimens of apatite, biotite, and oligoclase were buried in the organic, eluvial, and upper illuvial horizons of a podzol soil. After an incubation period of two years, the soil attached to the mineral surfaces was collected, and microbial communities were analyzed by means of Illumina MiSeq sequencing of the 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA genes. We found that both composition and diversity of bacterial, archaeal, and fungal communities varied across the different mineral surfaces, and that mineral type had a greater influence on structuring microbial assemblages than soil horizon. Thus, our findings emphasize the importance of mineral surfaces as ecological niches in soils.     

Spatial Organization of Microbial Biofilm Communities

Abstract The application of advanced microscopy and molecular and electrochemical high-resolution methods has provided insights into the structural organization and function of biofilm communities. It appears that cellular properties such as growth differentiation, chemotaxis, and cell-to-cell signaling enable biofilm communities to organize structurally in response to the external conditions and the activities of the different biofilm members. Thereby resource utilization becomes optimized, and processes which require syntrophic relationships or special micro-environments become facilitated. Received: 23 February 2000; Accepted: 8 June 2000; Online Publication: 28 August 2000     

Soil Microbial Communities of Eastern Antarctica

Investigation of microbial communities of Antarctica soils is a very important field of research that expands our knowledge of microbial participation in primary soil formation and specific features of their communities in extreme habitats, and it is of considerable interest in directed search of for microorganisms as potential biotechnological objects. The results of long-term (2012–2017) complex studies on soil microbial communities of the Russian East Antarctica polar stations at Shirmakher oasis (Novolazarevskaya station), the Larsemann Hills (Progress station), and the Tala Hills (Molodezhnaya station) are presented in this review. The assessment of biomass of soil microorganisms by the methods of direct microscopy has been carried out for the first time for this region. The general amount of microbial biomass is small; the fungi dominate (77–99%). The unique features of Antarctic soils are the high content and morphological diversity of small forms of microorganisms: fungi are presented by mainly single-celled structures (small spores and yeasts), while bacteria by ultrafine (filtering) forms. At the same time, microorganisms can significantly contribute to such important ecological functions of soil as the emission of greenhouse gases, especially during the warm season with the stable positive temperatures of the soil. This should be considered during creation of models and forecasts of global warming. The use of various isolation techniques for the analysis of the soil microbial population, together with the succession approach, significantly expand the information about taxonomic diversity of cultivated fungi and bacteria in Antarctica soils.     

Proteorhodopsin-Like Genes Present in Thermoacidophilic High-Mountain Microbial Communities

Proteorhodopsin (PR) sequences were PCR amplified from three Andean acidic hot spring samples. These sequences were similar to freshwater and marine PRs and they contained residues indicative of proton-pumping activity and of proteins that absorb green light; these findings suggest that PRs might contribute to cellular metabolism in these habitats.     

Characterization of Microbial Communities in Gas Industry Pipelines

Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion.     

矿山废水中微生物生态多样性研究

从湖北铜绿山铜矿和山西中条山铜矿两地采集了矿山废水样品, 用RFLP方法(限制性片段长度多态性方法)分析不同矿山废水中微生物多样性及其群落结构组成变化。结果发现：通过16S rDNA基因序列的系统发育树分析, 在5个矿山废水样品中检测到的细菌主要分为4大类：即Proteobacteria纲、Nitrospira纲、Firmicutes纲和Bacteroidetes纲。通过对古菌16S rDNA 的PCR分析发现, 取自湖北铜绿山铜矿的样品中检测到古菌的存在, 而取自山西中条山铜矿的样品中没有检测到古菌的存在。检测到的古菌主要是属于Ferroplasma属和Thermoplasma属。结合5个矿山废水样品的化学元素分析结果和细菌群落结构数据, 进行PCA分析(主成分分析), 发现不同矿山废水样品的生物地球化学性质及其微生物组成存在很大差异, pH值、温度、不同浓度的元素如S、Cu、Ni和Co可能是形成细菌种群结构差异的关键因素。     

Winter Planktonic Microbial Communities in Highland Aquatic Habitats

Winter conditions in aquatic habitats of the temperate zone markedly differ from those present in warmer seasons, nevertheless, relatively scarce information is available on planktonic microbial composition, as sites are not easily accessible and it was supposed traditionally that microbial activity is low during this cold period. Since microorganisms could have great impact on the ecosystem even during winter, we explored various sites in the Eastern Carpathians regarding the abundance and taxonomic composition of planktonic microorganisms. Although many of the studied environments were extreme habitats, planktonic microbial communities were abundant and mostly diverse with the presence of previously unidentified taxa.     

石油污染海域的微生物群落及烃的降解

目前世界海洋石油污染问题已经严重威胁到海洋生态环境的安全,生物修复是一种处理石油污染的新方法。综述了海洋环境中烃降解微生物生态学方面的一些研究进展,包括探测未培养细菌的新方法、新的分离方法及主要的烃降解菌株的特性,以便努力改进现有分离石油降解菌及石油乳化细菌的方法,同时发现对于石油降解有益的新菌种。     

Strain Identification and Quantitative Analysis in Microbial Communities

Microbiology has long studied the ways in which subtle genetic differences between closely related microbial strains can have profound impacts on their phenotypes and those of their surrounding environments and communities. Despite the growth in high-throughput microbial community profiling, however, such strain-level differences remain challenging to detect. Once detected, few quantitative approaches have been well-validated for associating strain variants from microbial communities with phenotypes of interest, such as medication usage, treatment efficacy, host environment, or health. First, the term “strain” itself is not used consistently when defining a highly-resolved taxonomic or genomic unit from within a microbial community. Second, computational methods for identifying such strains directly from shotgun metagenomics are difficult, with several possible reference- and assembly-based approaches available, each with different sensitivity/specificity tradeoffs. Finally, statistical challenges exist in using any of the resulting strain profiles for downstream analyses, which can include strain tracking, phylogenetic analysis, or genetic association studies. We provide an in depth discussion of recently available computational tools that can be applied for this task, as well as statistical models and gaps in performing and interpreting any of these three main types of studies using strain-resolved shotgun metagenomic profiling of microbial communities.     

Thermophilic Microbial Communities of Deep-Sea Hydrothermal Vents

The most recent publications on the phylogenetic and functional diversity of thermophilic prokaryotes inhabiting thermal deep-sea environments are reviewed. Along with a general physicochemical characterization of the biotope studied, certain adaptation mechanisms are discussed that are peculiar to the microorganisms inhabiting it. A separate chapter addresses the phylogenetic analysis of deep-sea hydrothermal microbial communities and uncultivated microorganisms recently discovered therein using molecular biological techniques. Physiological groups of thermophilic microorganisms found in deep-sea hydrothermal vents are considered: methanogens, sulfate-, iron-, and sulfur-reducers, aerobic hydrogen-oxidizing prokaryotes, aerobic and anaerobic organotrophs. In most cases, the isolates represent novel taxons.     

Impact of Fumigants on Soil Microbial Communities

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.     

Microbial Astronauts: Assembling Microbial Communities for Advanced Life Support Systems

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments everything is everywhere given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment.     

Aspects of Diversity Measurement for Microbial Communities

A useful measure of diversity was calculated for microbial communities collected from lake water and sediment samples using the Shannon index (H′) and rarefaction [E(S)]. Isolates were clustered by a numerical taxonomy approach in which limited (<20) tests were used so that the groups obtained represented a level of resolution other than species. The numerical value of diversity for each sample was affected by the number of tests used; however, the relative diversity compared among several sampling locations was the same whether 11 or 19 characters were examined. The number of isolates (i.e., sample size) strongly influenced the value of H′ so that unequal sized samples could not be compared. Rarefaction accounts for differences in sample size inherently so that such comparisons are made simple. Due to the type of sampling carried out by microbiologists, H′ is estimated and not determined and therefore requires a statement of error associated with it. Failure to report error provided potentially misleading results. Calculation of the variance of H′ is not a simple matter and may be impossible when handling a large number of samples. With rarefaction, the variance of E(S) is readily determined, facilitating the comparison of many samples.