Quantitative Properties of Random Amplified Polymorphic DNA (RAPD)

Random Amplified Polymorphic DNA analysis (RAPD) is a methodology that has been used as a tool for monitoring microbial communities. To be useful in this application RAPD, and any other methodology, must show properties that allows for the detection of quantitative changes in composition of the microbiota. Therefore, the objective of this study was to establish whether RAPD possesses such properties. The strategy was to use genomic DNA, extracted from a set of tertiary bacterial mixtures defined according to an experimental mixture design, and containing varying proportions of Escherichia coli, Bacillus subtilis, and Pseudomonas CF600. RAPD-PCR was performed on the mixed DNA extracts and the amplified DNA fragments were separated on sequencing gels to produce genomic fingerprints that were digitized and modeled by Partial Least Squares regression (PLS). Significant predictions were obtained using an external test set for validation, with Root Mean Square Error of Predictions (RMSEP) of 0.21, 0.19 and 0.20 for the proportion of E. coli, B. subtilis and Pseudomonas CF600 respectively. Taken together, the results showed that RAPD patterns quantitatively represented the initial mixture proportions. Therefore, the view that RAPD could be useful for whole microbial community monitoring was strengthened.     

Microbial diversity of boron-rich volcanic hot springs of St. Lucia, Lesser Antilles

The volcanic Sulphur Springs, St. Lucia, present an extreme environment due to high temperatures, low pH values, and high concentrations of sulfate and boron. St. Lucia offers some unique geochemical characteristics that may shape the microbial communities within the Sulphur Springs area. We chose six pools representing a range of geochemical characteristics for detailed microbial community analyses. Chemical concentrations varied greatly between sites. Microbial diversity was analyzed using 16S rRNA gene clone library analyses. With the exception of one pool with relatively low concentrations of dissolved ions, microbial diversity was very low, with Aquificales sequences dominating bacterial communities at most pools. The archaeal component of all pools was almost exclusively Acidianus spp. and did not vary between sites with different chemical characteristics. In the pool with the highest boron and sulfate concentrations, only archaeal sequences were detected. Compared with other sulfur springs such as those at Yellowstone, the microbial diversity at St. Lucia is very different, but it is similar to that at the nearby Lesser Antilles island of Montserrat. While high elemental concentrations seem to be related to differences in bacterial diversity here, similarities with other Lesser Antilles sites suggest that there may be a biogeographical component as well.     

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.     

Effects of Revegetation on Soil Microbial Biomass,Enzyme Activities,and Nutrient Cycling on the Loess Plateau in China

Revegetation is a traditional practice widely used for soil and water conservation on the Loess Plateau in China. However, there has been a lack of reports on soil microbial–biochemical indices required for a comprehensive evaluation of the success of revegetation systems. In this study, we examined the effects of revegetation on major soil nutrients and microbial–biochemical properties in an artificial alfalfa grassland, an enclosed natural grassland, and an artificial shrubland (Caragana korshinskii), with an abandoned cropland as control. Results showed that at 0–5, 5–20, and 20–40 cm depths, soil organic carbon, alkaline extractable nitrogen and available potassium were higher in natural grassland and artificial shrubland compared with artificial grassland and abandoned cropland. Soil microbial biomass C (Cmic) and phosphorous (Pmic) substantially decreased with depth at all sites, and in abandoned cropland was significantly lower than those of natural grassland, artificial grassland, and artificial shrubland at the depth of 0–5 cm. Soil microbial biomass N (Nmic) was higher in artificial shrubland and abandoned cropland compared with that in natural and artificial grasslands. Both Cmic and Pmic were significantly different between the 23‐year‐old and the 13‐year‐old artificial shrublands at the 0–5 cm depth. The activities of soil invertase, urease, and alkaline phosphatase in natural grassland and artificial shrubland were higher than those in artificial grassland and abandoned cropland. This study demonstrated that the regeneration of both natural grassland and artificial shrubland effectively preserved and enhanced soil microbial biomass and major nutrient cycling, thus is an ecologically beneficial practice for recovery of degraded soils on the Loess Plateau.     

微生物燃料电池在毒性物质检测中的应用

微生物燃料电池(Microbial fuel cell,MFC)利用微生物整体作为催化剂催化底物将化学能直接转化为电能,是一种极具应用前景的生物电化学技术。微生物在阳极氧化还原有机物产生电子并传递给阳极,电子通过外电路传递至阴极后将电子释放给阴极中的氧化剂,从而产生电流。当有毒物质进入MFC,微生物活性降低,电子传递量变少,电流降低,而电流的产生与微生物活性呈线性关系,据此可检测样品的毒性。本文主要介绍了微生物燃料电池在毒性物质抗生素、重金属离子、有机污染物、酸等方面的研究,并分析了微生物燃料电池存在的问题及未来研究方向,以期不久的将来微生物燃料电池能付之使用。     

Microbial Communities Associated with Tree Bark Foliose Lichens: A Perspective on their Microecology

Tree‐bark, foliose lichens occur widely on a global scale. In some locales, such as forests, they contribute a substantial amount of biomass. However, there are few research reports on microbial communities including eukaryotic microbes associated with foliose lichens. Lichens collected from tree bark at 11 locations (Florida, New York State, Germany, Australia, and the Arctic) were examined to determine the density and C‐biomass of bacteria and some eukaryotic microbes, i.e. heterotrophic nanoflagellates (HNF) and amoeboid protists. A rich microbial diversity was found, including large plasmodial slime molds, in some cases exceeding 100 μm in size. The densities of HNF and amoeboid protists were each positively correlated with densities of bacteria, r = 0.84 and 0.80, respectively (p < 0.01, N = 11 for each analysis) indicating a likely bacterial‐based food web. Microbial densities (number/g lichen dry weight) varied markedly across the geographic sampling sites: bacteria (0.7–13.1 × 10⁸), HNF (0.2–6.8 × 10⁶) and amoeboid protists (0.4–4.6 × 10³). The ranges in C‐biomass (μg/g lichen dry weight) across the 11 sites were: bacteria (8.8–158.5), HNF (0.03–0.85), and amoeboid protists (0.08–540), the latter broad range was due particularly to absence or presence of large slime mold plasmodia.     

Fe- and S-Metabolizing Microbial Communities Dominate an AMD-Contaminated River Ecosystem and Play Important Roles in Fe and S Cycling

Indigenous Fe- and S-metabolizing bacteria play important roles both in the formation and the natural attenuation of acid mine drainage (AMD). Due to its low pH and Fe-S-rich waters, a river located in the Dabaoshan Mine area provides an ideal opportunity to study indigenous Fe- and S-metabolizing microbial communities and their roles in biogeochemical Fe and S cycling. In this work, water and sediment samples were collected from the river for physicochemical, mineralogical, and microbiological analyses. Illumina MiSeq sequencing indicated higher species richness in the sediment than in the water. Sequencing also found that Fe- and S-metabolizing bacteria were the dominant microorganisms in the heavily and moderately contaminated areas. Fe- and S-metabolizing bacteria found in the water were aerobes or facultative anaerobes, including Acidithiobacillus, Acidiphilium, Thiomonas, Gallionella, and Leptospirillum. Fe- and S-metabolizing bacteria found in the sediment belong to microaerobes, facultative anaerobes, or obligatory anaerobes, including Acidithiobacillus, Sulfobacillus, Thiomonas, Gallionella, Geobacter, Geothrix, and Clostridium. Among the dominant genera in the sediment, Geobacter and Geothrix were rarely detected in AMD-contaminated natural environments. Canonical correspondence analysis indicated that pH, S, and Fe concentration gradients were the most important factors in structuring the river microbial community. Moreover, a scheme explaining the biogeochemical Fe and S cycling is advanced in light of the Fe and S species distribution and the identified Fe- and S-metabolizing bacteria.     

EFFECTS OF DISTURBANCE ON EPIPHYTIC COMMUNITY ARCHITECTURE1

Microdistributional patterns of attached algal communities on Cladophora and glass slides were compared under varying disturbance regimes in the Upper Mississippi River, using light and scanning electron microscopy. Localized physical disturbance, induced by boat traffic and wind-generated wave action in the main channel, inhibited development of complex attached algal communities and maintained an adnate flora with two-dimensional architecture. In contrast, communities protected from disturbance developed a more complex, three-dimensional architecture. A high degree of architectural similarity was observed between communities on Cladophora and glass substrates exposed to similar levels of disturbance. Communities exposed to severe disturbance resembled ones in early stages of colonization and development, whereas less disturbed communities were similar to ones in advanced stages of development. These results demonstrated that turbulence strongly influences the community structure of periphyton on both micro and macro scale levels.     

Usefulness of length heterogeneity-PCR for monitoring lactic acid bacteria succession during maize ensiling

The use of length-heterogeneity PCR was explored to monitor lactic acid bacteria succession during ensiling of maize. Bacterial diversity was studied during the fermentation of 30-day-old maize in optimal and spoilage-simulating conditions. A length heterogeneity PCR profile database of lactic acid bacteria isolated from the silage and identified by 16S rRNA gene sequencing was established. Although interoperonic 16S rRNA gene length polymorphisms were detected in some isolates, strain analysis showed that most of the lactic acid bacteria species thriving in silage could be discriminated by this method. The length heterogeneity PCR profiles of bacterial communities during maize fermentation were compared with those on a database. Under optimal fermentation conditions all the ecological indices of bacterial diversity, richness and evenness, deduced from community profiles, increased until day thirteen of fermentation and then decreased to the initial values. Pediococcus and Weissella dominated, especially in the first days of fermentation. Lactococcus lactis ssp. lactis and Lactobacillus brevis were mainly found after six days of fermentation. A peak corresponding to Lactobacillus plantarum was present in all the fermentation phases, but was only a minor fraction of the population. Unsuitable fermentation conditions and withered maize leaves in the presence of oxygen and water excess caused an enrichment of Enterococcus sp. and Enterobacter sp.     

Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.