Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P < 0.05). At Hillside, communities in surface soils (0.03- to 0.2-m depth) differed significantly with landform and land use (P < 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity.     

Geochemical Influence on Diversity and Microbial Processes in High Temperature Oil Reservoirs

The diversity of thermophilic microbial assemblages detected within two neighboring high temperature petroleum formations was shown to closely parallel the different geochemical regimes existing in each. A high percentage of archaeal 16S rRNA gene sequences, related to thermophilic aceticlastic and hydrogenotrophic methanogens, were detected in the natural gas producing Rincon Formation. In contrast, rRNA gene libraries from the highly sulfidogenic Monterey Formation contained primarily sulfur-utilizing and fermentative archaea and bacteria. In addition to the variations in microbial community structure, microbial activities measured in microcosm experiments using high temperature production fluids from oil-bearing formations also demonstrated fundamental differences in the terminal respiratory and redox processes. Provided with the same suite of basic energy substrates, production fluids from the South Elwood Rincon Formation actively generated methane, while thermophilic microflora within the Monterey production fluids were dominated by hydrogen sulfide producing microorganisms. In both cases, molecular hydrogen appeared to play a central role in the stimulation of carbon and sulfur cycling in these systems. In methanogenic production fluids, the addition of sulfur compounds induced a rapid shift in the terminal electron accepting process, stimulating hydrogen sulfide formation and illustrating the metabolic versatility of the subsurface thermophilic assemblage. The high similarity between microbial community structure and activity corresponding with the prevalent geochemical conditions observed in deep subsurface petroleum reservoirs suggests that the resident microflora have adapted to the subsurface physicochemical conditions and may actively influence the geochemical environment in situ.     

Microbial Diversity in Sediments of Saline Qinghai Lake, China: Linking Geochemical Controls to Microbial Ecology

Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on the Qinghai–Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40–70 mM) and dissolved organic carbon (1596–5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were ∼2 and <0.5%, respectively. Acridine orange direct count data indicated that cell numbers decreased from 4 × 10⁹ cells/g at the water–sediment interface to 6× 10⁷ cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in the bacterial community with depth. Whereas the α-, β-, and γ-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water–sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but thepresence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and clone sequences could be grouped inthe Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments. Acetate-utilizing methanogens were isolated from sediment incubations, and α- and γ-proteobacterial isolates were obtained from a water sample from the lakebottom (23 m). Our data collectively showed that the observed diversity and shift in the community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments.     

Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.     

Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits

Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation.     

Exploring Bacterial Diversity in Hospital Environments by GS-FLX Titanium Pyrosequencing

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.     

Distribution and Diversity of Symbiotic Thermophiles, Symbiobacterium thermophilum and Related Bacteria, in Natural Environments

Symbiobacterium thermophilum is a tryptophanase-positive thermophile which shows normal growth only in coculture with its supporting bacteria. Analysis of the 16S rRNA gene (rDNA) indicated that the bacterium belongs to a novel phylogenetic branch at the outermost position of the gram-positive bacterial group without clustering to any other known genus. Here we describe the distribution and diversity of S. thermophilum and related bacteria in the environment. Thermostable tryptophanase activity and amplification of the specific 16S rDNA fragment were effectively employed to detect the presence of Symbiobacterium. Enrichment with kanamycin raised detection sensitivity. Mixed cultures of thermophiles containing Symbiobacterium species were frequently obtained from compost, soil, animal feces, and contents in the intestinal tracts, as well as feeds. Phylogenetic analysis and denaturing gradient gel electrophoresis of the specific 16S rDNA amplicons revealed a diversity of this group of bacteria in the environment.     

Gut Microbial Diversity in Rat Model Induced by Rhubarb

Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (P<0.05). Furthermore, a 380 bp product was found to be increased in rhubarb-exposed rats both in faces and the bowel mucosa. The product was cloned and sequenced and showed high similarity with regions of the Bacteroides genome. AS a result of discriminant analysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established.     

Significant Biogenesis of Chlorinated Aromatics by Fungi in Natural Environments

Common wood- and forest litter-degrading fungi produce chlorinated anisyl metabolites. These compounds, which are structurally related to xenobiotic chloroaromatics, occur at high concentrations of approximately 75 mg of chlorinated anisyl metabolites kg of wood^-1 or litter^-1 in the environment. The widespread ability among common fungi to produce large amounts of chlorinated aromatic compounds in the environment makes us conclude that these kinds of compounds can no longer be considered to originate mainly from anthropogenic sources.     

Striking Natural Diversity in Glandular Trichome Acylsugar Composition Is Shaped by Variation at the Acyltransferase2 Locus in the Wild Tomato Solanum habrochaites

Acylsugars are polyesters of short- to medium-length acyl chains on sucrose or glucose backbones that are produced in secretory glandular trichomes of many solanaceous plants, including cultivated tomato (Solanum lycopersicum). Despite their roles in biotic stress adaptation and their wide taxonomic distribution, there is relatively little information about the diversity of these compounds and the genes responsible for their biosynthesis. In this study, acylsugar diversity was assessed for 80 accessions of the wild tomato species Solanum habrochaites from throughout the Andes Mountains. Trichome metabolites were analyzed by liquid chromatography-time of flight-mass spectrometry, revealing the presence of at least 34 structurally diverse acylsucroses and two acylglucoses. Distinct phenotypic classes were discovered that varied based on the presence of glucose or sucrose, the numbers and lengths of acyl chains, and the relative total amounts of acylsugars. The presence or absence of an acetyl chain on the acylsucrose hexose ring caused clustering of the accessions into two main groups. Analysis of the Acyltransferase2 gene (the apparent ortholog of Solyc01g105580) revealed differences in enzyme activity and gene expression correlated with polymorphism in S. habrochaites accessions that varied in acylsucrose acetylation. These results are consistent with the hypothesis that glandular trichome acylsugar acetylation is under selective pressure in some populations of S. habrochaites and that the gene mutates to inactivity in the absence of selection.Trichomes are specialized epidermal cells that protrude from the surface of a variety of plant tissues. They are thought to protect against environmental stresses such as herbivory (Kang et al., 2010a; Weinhold and Baldwin, 2011), loss of water through transpiration, and UV irradiation (Zhou et al., 2007). In particular, secreting glandular trichomes (SGTs) serve as “chemical factories” where specialized metabolites are produced, stored, or volatized (Wagner, 1991; Schilmiller et al., 2008, 2010a). In addition, SGTs produce and secrete proteins on the plant surface for insect protection (Yu et al., 1992; Thipyapong et al., 1997) and pathogen defense (Shepherd et al., 2005). SGTs also contribute to the taste and smell of plants by releasing volatile metabolites. For example, the distinctive aromas of many Mediterranean herbs of the Lamiaceae (mint family) derive from SGTs (Schilmiller et al., 2008), and compounds from the glands of hops (Humulus lupulus in the Cannabaceae) contribute to beer flavor and aroma (Wang et al., 2008). Furthermore, a number of SGT-borne metabolites are commercially valuable, especially for pharmaceutical purposes. For example, artemisinin, a widely used antimalarial, is a sesquiterpene lactone from the trichomes of Artemisia annua (Liu et al., 2011). In addition to their value in foods and medicines, trichomes provide excellent models for analyzing biosynthetic enzymes and pathways (Schilmiller et al., 2008, 2009, 2012b; Bohlmann and Gershenzon, 2009; Sallaud et al., 2009).Plants in the genus Solanum include important crop species such as potato (Solanum tuberosum), eggplant (Solanum melongena), and tomato (Solanum lycopersicum). Previous studies reported that SGTs of cultivated tomato and its wild relatives accumulate high levels of exudates containing a variety of specialized metabolites, for example flavonoids, alkaloids, and terpenoids (Wagner, 1991; Schilmiller et al., 2008, 2010a; McDowell et al., 2011). Cultivated tomato and its wild relatives have morphologically and chemically diverse trichomes. For example, Luckwill (1943) defined seven morphologically distinguishable types of trichomes in plants of this genus, including four glandular types (types 1, 4, 6, and 7; Supplemental Fig. S1; for more Solanum spp. trichome images, see Kang et al., 2010a, 2010b). The presence of specific types of trichomes and their densities vary across species and even within a single plant according to tissue types, developmental stages, and environmental conditions (Werker, 2000; Li et al., 2004). These morphologically distinct SGTs vary in the amounts and types of metabolites that they produce, accumulate, and/or secrete (Werker, 2000). For example, S. lycopersicum M82 leaf type 6 SGTs accumulate the sesquiterpenes β-caryophyllene and α-humulene, while the glands on the stem lack these metabolites (Schilmiller et al., 2010b). There are also species- and accession-specific differences in SGT metabolite profiles. For instance, methylketones accumulate in type 6 glands of a subset of Solanum habrochaites accessions (Fridman et al., 2005; Yu et al., 2010). Similarly, acylglucoses are highly abundant in type 4 glands of Solanum pennellii LA0716, while acylsucroses predominate in S. lycopersicum and S. habrochaites (Shapiro et al., 1994; McDowell et al., 2011). The chemical and morphological diversity of trichomes in different Solanum species and accessions makes the genus an attractive target for the identification of diverse trichome-borne metabolites and the major biosynthetic pathways responsible for their synthesis operating in each trichome type.The value of the comparative metabolomics approach in trichomes was recently demonstrated in studies of Solanum spp. trichome monoterpene and sesquiterpene biosynthesis (Bohlmann and Gershenzon, 2009; Sallaud et al., 2009; Schilmiller et al., 2009). It was discovered that S. lycopersicum SGTs synthesize monoterpenes from the cis-prenyldiphosphate intermediate neryldiphosphate (Sallaud et al., 2009; Schilmiller et al., 2009). This is contrary to the previous paradigm, where the trans-prenyldiphosphate geranyldiphosphate was considered the universal intermediate for monoterpene biosynthesis. An analogous example of biosynthetic innovation was reported for SGTs of S. habrochaites LA1777 (Sallaud et al., 2009), shown to produce sesquiterpenes in the plastid using the all-cis-prenyldiphosphate substrate Z,Z-farnesyldiphosphate. This is counter to the commonly described cytosolic sesquiterpene pathway, which uses the all-trans-sesquiterpene synthase substrate E,E-farnesyldiphosphate. Furthermore, a recent study demonstrated chemical diversity of trichome terpenes in geographically distinct S. habrochaites accessions associated with the evolution of terpene synthases, revealing how the plasticity of biosynthetic enzymes contributes to chemical complexity and diversity (Gonzales-Vigil et al., 2012). These observations suggest that trichome specialized metabolism is evolutionarily plastic, perhaps due to selective pressure from insects or other environmental stress agents.Acylsugars are sticky exudates made in SGTs that are thought to physically or chemically improve plant defense (Mirnezhad et al., 2010; Weinhold and Baldwin, 2011). Results from the literature indicate strong acylsugar diversity in various Solanum spp. trichomes (Schilmiller et al., 2010a, 2010b; McDowell et al., 2011). Acylsugars are categorized as either Suc or Glc esters based on the type of sugar core (Fig. 1), and they also have varying numbers and lengths of acyl chains decorating the sugar moiety. In particular, S. pennellii accumulates enormous amounts of acylsugars, up to 20% of leaf dry weight (Fobes et al., 1985). In addition, previously published data showed that total acylsugars in geographically distinct S. pennellii accessions vary in quantity, the proportion of Suc or Glc backbones, and the overall types of fatty acid esters (FAs) on the sugars (Shapiro et al., 1994). However, this study did not identify specific acylsugar types.Open in a separate windowFigure 1.Structural classes of acylsugars in Solanum species. A, Schematic structure of an acylglucose. The structure shown depicts a Glc triester composed of Glc and three acyl chains with various numbers of carbons represented as R. B, Schematic structure of an acylsucrose. The proposed structure shows a Suc tetraester with three acyl chains on the Glc ring and one on the Fru ring. If the sugar moiety is decorated with three, four, or five acyl chains, it is referred to as a Suc triester, tetraester, or pentaester, respectively. The positions of the acyl chains are currently unknown, with the exception of the most abundant acylsugar in cultivated tomato (M82) that was structurally characterized by NMR (Schilmiller et al., 2010a). In addition, a few acylsugars were isolated and reported from S. habrochaites and other species by King et al. (1990, 1993). Note the changes in nomenclature since these papers were published: Lycopersicum typicum LA1777 is now called S. habrochaites LA1777, and Lycopersicum hirsutum has been changed to S. habrochaites.To explore the detailed acylsugar chemotypes within accessions of one species, we focused on 80 accessions collected throughout the geographical range of S. habrochaites in Peru and Ecuador (Supplemental Table S1). We describe differences in sugar backbone as well as numbers and lengths of acyl chains, including the presence or absence of an acetyl group, which we found to be a major difference in accessions from the southern and northern Andes Mountains. The recent identification of the acyltransferase2 enzyme (SlAT2; encoded by Solyc01g105580), involved in acylsucrose biosynthesis in S. lycopersicum (Schilmiller et al., 2012a), permitted a test of the hypothesis that differences in expression or activity of this enzyme play an important role in the chemical diversity observed. The results extend previous evidence that Solanum spp. SGT chemistry is highly dynamic (Gonzales-Vigil et al., 2012) and show that the AT2 gene is surprisingly diverse across populations of S. habrochaites.     

Characterization of Microbial Diversity in Hypersaline Environments by Melting Profiles and Reassociation Kinetics in Combination with Terminal Restriction Fragment Length Polymorphism (T-RFLP)

The diversity of prokaryotes inhabiting solar saltern ponds was determined by thermal melting and reassociation of community DNA. These measurements were compared with fingerprinting techniques such as terminal restriction fragment length polymorphisms (T-RFLP) analysis, denaturant gradient gel electrophoresis (DGGE), and cloning and sequencing approaches. Three ponds with salinities of 22, 32, and 37% (NaCl saturation) were studied. The combination of independent molecular techniques to estimate the total genetic diversity provided a realistic assessment to reveal the microbial diversity in these environments. The changes in the prokaryotic communities at different salinity (22, 32, and 37% salt) were significant and revealed that the total genetic diversity increased from 22% to 32% salinity. At 37% salinity the diversity was reduced again to nearly half that at 22% salinity. Our results revealed that the community genome had a DNA complexity that was 7 (in 22% salinity pond), 13 (in 32% salinity pond), and 4 (in 37% salinity pond) times the complexity of an Escherichia coli genome. The base composition profiles showed two abundant populations, which changed in relative amount between the three ponds. They indicated an uneven taxon distribution at 22% and 37% salinity and a more even distribution at 32% salinity. The results indicated a large predominating population at 37% salinity, which might correspond to the abundance of square archaea (SPhT) observed by transmission electron microscopy (TEM) and also indicated by the same T-RFLP fragment as the SPhT. The SPhT phylotype has also been reported to be the most frequently retrieved phylotype from this environment by culture independent techniques. In addition, two different operational taxonomic units (OTU) were detected at 37% salinity based on PCR with bacterial specific primers and T-RFLP. One of these predominant phylotypes is the extreme halophilic bacterium belonging to the bacteroidetes group, Salinibacter ruber.     

The Genetical Response to Natural Selection by Varied Environments. IV. Gametic Disequilibrium in Spatially Varied Environments

Gametic disequilibria between allozyme loci were related to spatial variation of the environment in caged populations of Drosophila melanogaster . Two experiments, one with flies collected at "Chateau Tahbilk," South Australia, and the other with flies from "Groningen," The Netherlands, were sampled at generations 16 and 32. Spatial variation of the environment was stimulated using three food media. Eight polymorphic allozyme loci were used to estimate gametic disequilibria from digenic combinations of allotypes. All populations were duplicated within an environment and maintained at about 2500 adults. Standardized gametic disequilibria were compared by a weighted least squares analysis of the z-transformed statistical correlation of allele frequencies. Gametic disequilibria were strongly dependent upon food niche and food-niche interactions. The effects also varied with sampling time and were similar in duplicate populations. Gametic disequilibria were most often detected in the "Groningen"-derived populations and their strength was not strongly associated with recombination fraction. Many of the disequilibria concerned unlinked loci. The strength of selection was probably considerable and populations were evolving genetic architectures which reflected niche selection by the different foods without marked genetic isolation between foods; gene frequencies did not vary between niches within a population cage.     

DGGE技术在环境微生物多样性研究中的应用

微生物是污水净化的主要作用者之一.采用变性梯度凝胶电泳(denaturing gradient gel electrophresis,DGGE)方法培育和鉴定土壤微生物具有可靠性强、重复性好、方便快捷等优点,已被广泛应用于环境科学和污染防治研究领域.综述了基于PCR-DGGE技术的基本原理、关键环节及其在微生物多样性研究中的应用,同时就其自身存在的不足进行了评价并提出了解决方案.     

PCR-RFLP法探讨三个人工湖微生物群落多样性

目的：探讨牡丹江市区三个人工湖（月牙湖、牛角湖、南湖）的微生物群落多样性。方法：从三个水样中分别提取微生物DNA,选取通用引物扩增16S rDNA片段,对扩增产物进行RFLP分析。结果：不同的样品由于其中的微生物多样性的差异,酶切产物在凝胶上显示的相对位置和条带数目都有一定差异。结论：牛角湖样品的条带数目最多,表明牛角湖的微生物群落多样性最为丰富。     

Frequency of Antibiotic-Producing Pseudomonas spp. in Natural Environments

The antibiotics phenazine-1-carboxylic acid (PCA) and 2,4-diacetylphloroglucinol (Phl) are major determinants of biological control of soilborne plant pathogens by various strains of fluorescent Pseudomonas spp. In this study, we described primers and probes that enable specific and efficient detection of a wide variety of fluorescent Pseudomonas strains that produce various phenazine antibiotics or Phl. PCR analysis and Southern hybridization demonstrated that specific genes within the biosynthetic loci for Phl and PCA are conserved among various Pseudomonas strains of worldwide origin. The frequency of Phl- and PCA-producing fluorescent pseudomonads was determined on roots of wheat grown in three soils suppressive to take-all disease of wheat and four soils conducive to take-all by colony hybridization followed by PCR. Phenazine-producing strains were not detected on roots from any of the soils. However, Phl-producing fluorescent pseudomonads were isolated from all three take-all-suppressive soils at densities ranging from approximately 5 x 10(sup5) to 2 x 10(sup6) CFU per g of root. In the complementary conducive soils, Phl-producing pseudomonads were not detected or were detected at densities at least 40-fold lower than those in the suppressive soils. We speculate that fluorescent Pseudomonas spp. that produce Phl play an important role in the natural suppressiveness of these soils to take-all disease of wheat.     

Microbial Activity in Aquatic Environments Measured by Dimethyl Sulfoxide Reduction and Intercomparison with Commonly Used Methods

A new method to determine microbial (bacterial and fungal) activity in various freshwater habitats is described. Based on microbial reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), our DMSO reduction method allows measurement of the respiratory activity in interstitial water, as well as in the water column. DMSO is added to water samples at a concentration (0.75% [vol/vol] or 106 mM) high enough to compete with other naturally occurring electron acceptors, as determined with oxygen and nitrate, without stimulating or inhibiting microbial activity. Addition of NaN₃, KCN, and formaldehyde, as well as autoclaving, inhibited the production of DMS, which proves that the reduction of DMSO is a biotic process. DMSO reduction is readily detectable via the formation of DMS even at low microbial activities. All water samples showed significant DMSO reduction over several hours. Microbially reduced DMSO is recovered in the form of DMS from water samples by a purge and trap system and is quantified by gas chromatography and detection with a flame photometric detector. The DMSO reduction method was compared with other methods commonly used for assessment of microbial activity. DMSO reduction activity correlated well with bacterial production in predator-free batch cultures. Cell-production-specific DMSO reduction rates did not differ significantly in batch cultures with different nutrient regimes but were different in different growth phases. Overall, a cell-production-specific DMSO reduction rate of 1.26 × 10⁻¹⁷ ± 0.12 × 10⁻¹⁷ mol of DMS per produced cell (mean ± standard error; R² = 0.78) was calculated. We suggest that the relationship of DMSO reduction rates to thymidine and leucine incorporation is linear (the R² values ranged from 0.783 to 0.944), whereas there is an exponential relationship between DMSO reduction rates and glucose uptake, as well as incorporation (the R² values ranged from 0.821 to 0.931). Based on our results, we conclude that the DMSO reduction method is a nonradioactive alternative to other methods commonly used to assess microbial activity.     

Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptide-like biosynthetic gene clusters from Actinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities.     

分子生物学在石油微生物多样性研究中的应用

该文较系统地概述了目前以16SrRNA为基础的核酸探针检测技术、利用引物的PCR技术、DNA序列分析技术和电泳分离及显示技术在油藏微生物群落多样性和石油环境污染研究中的研究进展,并探讨了未来分子生物学技术在石油微生物研究中的发展方向。