Characteristics of foliar fungal endophyte assemblages and host effective components in Salvia miltiorrhiza Bunge

Salvia miltiorrhiza Bunge, a well-known medicinal plant, has more than 20 effective components. The aim of this study was to comprehensively investigate foliar fungal endophyte communities of S. miltiorrhiza and explore the inside relationship between host-specific fungal endophytes and effective components accumulation. Five plant samples were collected from four geological different provinces in China. Foliar fungal endophyte communities were determined by terminal restriction fragment length polymorphism (T-RFLP) of the ITS region. Effective components were analyzed with high-performance liquid chromatography. The results showed that S. miltiorrhiza foliage harbored a large diversity of fungal endophytes. Principal component analysis revealed similar T-RFLP profiles and the characteristics of the 24 effective components among the five samples, which could be clustered into three groups. In foliar T-RFLP profiles derived from the restriction digestion by CfoI, HaeIII, MspI, or TaqI, there were identical 45, 42, 38, and 34 terminal restriction fragments (T-RFs) from the five samples. We consider these T-RFs as host-specific fungal endophytes. Correlation analysis of these T-RFs’ area and 24 effective components contents revealed a significant correlationship between some host-specific fungal endophytes and foliage or root effective components accumulation.     

Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure

Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology. In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency. A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs. These peaks were called “pseudo-T-RFs” since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis. Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts. Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs. This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes. The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes. In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes. The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity. Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.     

Novel Bacterial Lineages at the (Sub)Division Level as Detected by Signature Nucleotide-Targeted Recovery of 16S rRNA Genes from Bulk Soil and Rice Roots of Flooded Rice Microcosms

Using a newly developed 16S rRNA gene (rDNA)-targeted PCR assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. For comparison, oxic rice roots were included as an additional sample in this investigation. The bacterial diversity detectable by this PCR assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (T-RFLP) analysis and comparative sequence analysis of cloned 16S rDNA. T-RFLP fingerprint patterns generated from rice roots contained 12 distinct terminal restriction fragments (T-RFs). In contrast, the T-RFLP fingerprint patterns obtained from the anoxic bulk soil contained 33 distinct T-RFs, a clearly higher level of complexity. A survey of 176 bulk soil 16S rDNA clone sequences permitted correlation of 20 T-RFs with phylogenetic information. The other 13 T-RFs remained unidentified. The predominant T-RFs obtained from rice roots could be assigned to members of the genus Pirellula within the Planctomycetales, while most of the T-RFs obtained from the bulk soil corresponded to novel lines of bacterial descent. Using a level of 16S rDNA sequence dissimilarity to cultured microorganisms of approximately 20% as a threshold value, we detected 11 distinct bacterial lineages for which pure-culture representatives are not known. Four of these lineages could be assigned to the order Planctomycetales, while one lineage was affiliated with the division Verrucomicrobia and one lineage was affiliated with the spirochetes. The other five lineages either could not be assigned to any of the main lines of bacterial descent or clearly expanded the known diversity of division level lineages WS3 and OP3. Our results indicate the presence of bacterial diversity at a subdivision and/or division level that has not been detected previously by the so-called universal 16S rDNA PCR assays.     

Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

Steep vertical gradients of oxidants (O₂ and NO₃⁻) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities.     

Movement and Fixation of Intestinal Microbiota after Administration of Human Feces to Germfree Mice

Human flora-associated (HFA) mice have been considered a tool for studying the ecology and metabolism of intestinal bacteria in humans, although they have some limitations as a model. Shifts in dominant species of microbiota in HFA mice after the administration of human intestinal microbiota was revealed by 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses. Characteristic terminal restriction fragments (T-RFs) were quantified as the proportion of total peak area of all T-RFs. Only the proportion of the T-RF peak at bp 366, identified as the Gammmaproteobacteria group and the family Coriobacteriaceae, was reduced in this study. Increased T-RFs over time at bp 56, 184, and 196 were affiliated with the Clostridium group. However, most of the isolated bacteria with unique population shifts were phylotypes. The vertical transmission of the intestinal microbiota of the mouse offspring was also investigated by dendrogram analysis derived from the similarity of T-RFLP patterns among samples. As a result, the intestinal microbiota of HFA mice and their offspring reflected the composition of individual human intestinal bacteria with some modifications. Moreover, we revealed that human-derived lactobacilli (HDL), which have been considered difficult to colonize in the HFA mouse intestine in previous studies based on culture methods, could be detected in the HFA mouse intestine by using a lactic acid bacterium-specific primer and HDL-specific primers. Our results indicate that the intestinal microbiota of HFA mice represents a limited sample of bacteria from the human source and are selected by unknown interactions between the host and bacteria.     

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.     

Pattern of soil methanotrophs on the natural vertical zones of the North Tianshan Mountain

Methane is one of the most important greenhouse gases and plays an essential role in atmospheric chemistry. Knowledge about methanotrophs and their diversity is important to understand the microbial mediation of the greenhouse gas CH₄ under climate change. The methanotrophs is one of main functional microbial groups in soil mediating methane cycles of terrestrial ecosystem. The purpose of this study was to explore spatial distribution pattern of methanotrophs diversity and the major factors affecting soil methanotrophs diversity along an elevation gradient on vertical natural belt of the North Tianshan Mountains, soil samples were collected at six sites in 2010, which were desert grassland belt (H1), Mountain grassland belt (H2), Mountain forest belt (H3), sub-alpine cushion belt (H4), alpine cushion belt (H5), alpine tundra vegetation (H6). Methanotrophs diversity in six sites from the North Tianshan Mountain were assessed with terminal restriction fragment length polymorphism (T-RFLP).The carbon–nitrogen ratio was significant difference under different vertical natural belt, ranged from 10.34 to 20.10, soil organic carbon were lowest in alpine tundra vegetation and highest in Mountain forest belt, those numbers of belts ranging from H1 to H3 were increased, with increasing elevation, then H3 to H6 were decreased. The total number of Terminal Restriction Fragments (T-RFs) derived from all those soil samples was 233, indicating high genetic diversity of methanotrophs on vertical natural belt of the North Tianshan Mountains. Microbial communities of T-RFs 55 bp, 242 bp, 376 bp represented the dominant species in sampling sites. However, some of the T-RFs were more sensitive to environment, such as 79 bp, 176 bp and 250 bp. Methanotrophs diversity index and T-RFs numbers were lowest in mountain forest belt and highest in subalpine cushion belt. Along the elevation gradient, the trendency of those numbers are as follows, H1>H2>H3<H4>H5>H6. Cluster analysis revealed that the samples could be separated into two groups, H4, H5 and H6 clustered into one group, while H2 and H3 clustered into other group.The community shifts were further investigated by Principle component analysis (PCA). The first PCA axis, which is related to the main compositional variation, separated the communities of the different sites. The main variation was mainly caused by changes in the relative abundance of the 58 bp, 87 bp, 137 bp, 243 bp and 248 bp T-RFs.Based on canonical correspondence analysis (CCA), Shannon index(H) of methanotrophs was positively correlated with soil pH and C/N ratio and negatively correlated with elevation, content of total nitrogen and total phosphorus; and Simpson index (D) and Evenness (E) were positively correlated with soils’ C/N ratio, soil surface temperature, pH and organic carbon, and negatively with elevation, total nitrogen and total phosphorus; indicating that plant communities and soil nutrients influence the soil microbial structure.Our research showed that soil methanotrophs was high genetic diversity along the elevation gradient on vertical natural belt in the North Tianshan Mountain. Soil microorganisms were positively correlated with vegetation, soils pH, C/N ratio, and soil moisture, total nitrogen, these parameters might be the main factors controlling soil methanotrophs diversity.     

Dynamics of Bacterial and Fungal Communities on Decaying Salt Marsh Grass

Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated microbial community. Here we describe the bacterial and fungal assemblages associated with two decomposition stages of Spartina alterniflora detritus in a productive southeastern U.S. salt marsh. 16S rRNA genes and 18S-to-28S internal transcribed spacer (ITS) regions were used to target the bacterial and ascomycete fungal communities, respectively, based on DNA sequence analysis of isolates and environmental clones and by using community fingerprinting based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Seven major bacterial taxa (six affiliated with the α-Proteobacteria and one with the Cytophagales) and four major fungal taxa were identified over five sample dates spanning 13 months. Fungal terminal restriction fragments (T-RFs) were informative at the species level; however, bacterial T-RFs frequently comprised a number of related genera. Amplicon abundances indicated that the salt marsh saprophyte communities have little-to-moderate variability spatially or with decomposition stage, but considerable variability temporally. However, the temporal variability could not be readily explained by either successional shifts or simple relationships with environmental factors. Significant correlations in abundance (both positive and negative) were found among dominant fungal and bacterial taxa that possibly indicate ecological interactions between decomposer organisms. Most associations involved one of four microbial taxa: two groups of bacteria affiliated with the α-Proteobacteria and two ascomycete fungi (Phaeosphaeria spartinicola and environmental isolate “4clt”).     

Formation of pseudo-terminal restriction fragments,a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure

Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology. In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency. A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs. These peaks were called "pseudo-T-RFs" since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis. Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts. Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs. This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes. The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes. In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes. The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity. Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.     

TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets

We describe TRiFLe, a freely accessible computer program that generates theoretical terminal restriction fragments (T-RFs) from any user-supplied sequence set tailored to a particular group of organisms, sequences from clone libraries, or sequences from specific genes. The program allows a rapid identification of the most polymorphic enzymes, creates a collection of T-RFs for the data set, and can potentially identify specific T-RFs in T-RF length polymorphism (T-RFLP) patterns by comparing theoretical and experimental results. TRiFLE was used for analyzing T-RFLP data generated for the amoA and pmoA genes. The peaks identified in the T-RFLP patterns show an overlap of ammonia- and methane-oxidizing bacteria in the metalimnion of a subtropical lake.     

Variability of ecological and autotrophic host specificity in a mycoheterotrophic system: Pterospora andromedea and associated fungal and conifer hosts

Few studies of tripartite mycoheterotrophic systems have examined ecological specificity across broad geographic ranges or addressed autotrophic host specificity. Pterospora andromedea was selected as an ideal candidate to examine ecological specificity of a mycoheterotrophic system as it is widely distributed, has been shown to have high levels of symbiont specificity with Rhizopogon subgenus Amylopogon, and is found with several autotrophic hosts. Pairs of P. andromedea + Rhizopogon spp. samples were co-collected across North America and were sequenced using trnL and ITS, respectively. Bayesian phylogenetic reconstructions between the co-collected taxa were used to examine ecological specificity, and for subsequent tests for autotroph specificity. P. andromedea lineages exhibited both high specificity and relaxed specificity for fungal symbionts and autotrophic hosts across the geographic landscape under allopatric and sympatric conditions. This strong evidence for geographic mosaics of specificity in mycoheterotrophic systems is an important future consideration in determining the evolutionary ecology of mycoheterotrophs.     

Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China

The effects of salt stress on endophytic prokaryotic communities in plants are largely unknown, and the distribution patterns of bacterial and archaeal endophytes in different tissues of a plant species are rarely compared. We investigated the endophytic bacterial and archaeal communities in roots, stems and leaves of the common reed, Phragmites australis, collected from three tidal zones along a salinity gradient, using terminal restriction fragment (T-RF) length polymorphism analysis of the 16S rRNA genes. The results showed that the bacterial diversity in the roots was significantly higher than that in the leaves, whereas similar archaeal diversity was revealed for either plant tissues or tidal zones. Network analysis revealed that T-RFs were grouped largely by tissue, and the major groups were generally linked by a few common T-RFs. Unique T-RFs in roots were mainly present in plants growing in the supratidal zone, but unique T-RFs in stems and leaves were mainly present in those from the middle and high tidal zones. Non-metric multidimensional scaling ordination and analysis of similarity revealed that bacterial communities were significantly different among tissues (P < 0.05), but similar among tidal zones (P = 0.49). However, the archaeal communities differed among tidal zones (P < 0.05), but were similar among tissues (P = 0.89). This study indicates that: (1) the endophytic archaeal communities are influenced more significantly than the endophytic bacterial communities by soil salinity, and (2) the differential distribution patterns of bacterial and archaeal endophytes in plant tissues along a salinity gradient imply that these two groups play different roles in coastal hydrophytes.     

Small-scale spatial heterogeneity of arbuscular mycorrhizal fungal abundance and community composition in a wetland plant community

Although it has become increasingly clear that arbuscular mycorrhizal fungi (AMF) play important roles in population, community, and ecosystem ecology, there is limited information on the spatial structure of the community composition of AMF in the field. We assessed small-scale spatial variation in the abundance and molecular diversity of AMF in a calcareous fen, where strong underlying environmental gradients such as depth to water table may influence AMF. Throughout an intensively sampled 2 × 2 m plot, we assessed AMF inoculum potential at a depth of 0–6 and 6–12 cm and molecular diversity of the AMF community using terminal restriction fragment length polymorphism of 18S rDNA. Inoculum potential was only significantly spatially autocorrelated at a depth of 6–12 cm and was significantly positively correlated with depth to water table at both depths. Molecular diversity of the AMF community was highly variable within the plot, ranging from 2–14 terminal restriction fragments (T-RFs) per core, but the number of T-RFs did not relate to water table or plant species richness. Plant community composition was spatially autocorrelated at small scales, but AMF community composition showed no significant spatial autocorrelation. Saturated soils of calcareous fens contain many infective AMF propagules and the abundance and diversity of AMF inoculum is patchy over small spatial scales. An erratum to this article can be found at     

越冬和复苏时期太湖水体蓝藻群落结构的时空变化

为研究太湖蓝藻在越冬与复苏时期群落结构的时空变化规律,于2008年11月,2009年2月,2009年4月,在太湖富营养化较严重的湖区选取8个采样点 (梅梁湾、竺山湾、贡湖湾、大浦、西太湖、南太湖、湖心和湖湾交汇处),分3层采水样,过滤并提取样品DNA经PCR扩增蓝藻16S rDNA序列,采用T-RFLP(末端标记的限制性酶切片段长度多样性)技术分析蓝藻群落结构和多样性变化。共得到87个不同的T-RFs(末端限制性酶切片段),表明太湖蓝藻具有丰富的基因多样性。T-RF相对丰度和聚类分析结果表明,太湖蓝藻群落结构在垂直空间上相似性较高,相似度 > 50%;在水平空间,与Microcystis spp.对应的信号峰在8个采样点均为最强峰(相对丰度为17.7% 47.5%)。竺山湾蓝藻多样性最低,西太湖最高,但其余采样点间蓝藻群落和Shannon多样性指数没有显著差异(P>0.05)。Microcystis相对丰度与Shannon多样性指数呈显著负相关(皮尔逊相关系数为-0.958)。在时间尺度上,相似性分析(Analysis of similarity,ANOSIM)结果显示太湖蓝藻群落结构存在极显著差异( P<0.01) 。春季复苏时蓝藻多样性最高,秋季衰亡时最低。聚类分析表明样品聚成两大特征类群,秋季衰亡时样品独自聚为1支,而春季复苏期和冬季越冬期样品彼此混杂。     

Changes in Bacterial Community Structure in the Colon of Pigs Fed Different Experimental Diets and after Infection with Brachyspira hyodysenteriae

Bacterial communities in the large intestines of pigs were compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S ribosomal DNA. The pigs were fed different experimental diets based on either modified standard feed or cooked rice supplemented with dietary fibers. After feeding of the animals with the experimental diets for 2 weeks, differences in the bacterial community structure in the spiral colon were detected in the form of different profiles of terminal restriction fragments (T-RFs). Some of the T-RFs were universally distributed, i.e., they were found in all samples, while others varied in distribution and were related to specific diets. The reproducibility of the T-RFLP profiles between individual animals within the diet groups was high. In the control group, the profiles remained unchanged throughout the experiment and were similar between two independent but identical experiments. When the animals were experimentally infected with Brachyspira hyodysenteriae, causing swine dysentery, many of the T-RFs fluctuated, suggesting a destabilization of the microbial community.     

How life history affects threat status: Requirements of two Onobrychis-feeding lycaenid butterflies, Polyommatus damon and Polyommatus thersites, in the Czech Republic

Comparisons of related species differing in conservation status may offer insights into causes of species declines. We studied egg-laying patterns and landscape occupancy of two sympatric lycaenidae butterflies inhabiting xeric grasslands, vulnerable Polyommatus thersites and critically endangered Polyommatus [Agrodiaetus] damon, both developing on sainfoin, Onobrychis spp. Females of bivoltine P. thersites oviposit on host plant leaves at a relatively low height (??20 cm), in both spring (May?CJune) and summer (July?CAugust) generations. Females of univoltine P. damon (July?CSeptember) oviposit to senescing inflorescences, in significantly higher heights (>30 cm), and the species is hence vulnerable to summer mowing or grazing. On a landscape scale, both species tended to occur at sites with diverse sward management, including temporarily unmanaged patches. In addition, P. damon occurred only in the proximity of other occupied sites. The study documents that grassland management must respect the needs of the most vulnerable species, and because these needs are seldom known, it must maintain a high diversity of conditions within individual sites.     

Characterization of Trichodesmium spp. by Genetic Techniques

The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus Trichodesmium. The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of Katagnymene. Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.     

Correlation of Functional Instability and Community Dynamics in Denitrifying Dispersed-Growth Reactors

Understanding the relationship between microbial community dynamics and functional instability is an important step towards designing reliable biological water treatment systems. In this study, the community dynamics of two dispersed-growth denitrifying reactors were examined during periods of functional stability and instability. In both reactors during the period of functional instability, the effluent chemistry changed over time, with periods of high nitrate concentrations followed by periods of fluctuating nitrite concentrations. Community structure was examined by clone library analysis of the 16S rRNA gene. Community dynamics were investigated with terminal restriction fragment (T-RF) length polymorphism, and the functional diversity represented by T-RFs was assessed through nitrate reduction assays of representative isolates. During the period of functional instability, the community structure changed considerably, and the dynamics correlated significantly with effluent chemistry. The nitrite concentration was significantly correlated with the relative abundances of the nitrate-reducing Delftia- and Achromobacter-like T-RFs. The isolate representing the Acidovorax-like T-RF reduced nitrate directly to nitrogen in batch assays without the accumulation of any intermediates. The Acidovorax-like T-RF relative abundance was significantly negatively correlated with nitrite concentration, indicating that it was associated with good functional performance. The results of this study reveal a clear relationship between community dynamics and functional instability and the importance of diversity among nitrate-reducing populations within a denitrifying community.     

Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire

This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH₃-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.     

Forest cover and heterogeneous pastures shape the diversity of predatory rove beetles in tropical riparian habitats

In tropical landscapes, forest remnants have been reduced to narrow strips of vegetation along rivers and streams surrounded by agricultural land that affects biodiversity, depending on the habitat and landscape characteristics. To assess the effect of riparian forest loss on the diversity of Staphylininae predatory rove beetles, we considered two habitat conditions (river sites with riparian vegetation and sites with heterogeneous pastures) within two micro-basin types (with >70% and <40% forest cover) in a tropical montane cloud forest landscape, Mexico. Beetles were collected using baited pitfall traps during the rainy season of 2014. No differences were found between micro-basin types and, although species richness (⁰D) was similar between habitat conditions, when the diversity of common (¹D) and dominant (²D) species was considered, sites with heterogeneous pastures were almost twice as diverse as those with riparian vegetation. All diversity measurements were greater in sites with heterogeneous pastures of either micro-basin type. Air temperature and canopy cover were the environmental variables that best explained the variation in beetle species composition. The greatest environmental differences related to species composition were detected between habitat conditions and were more evident in sites with heterogeneous pastures and low forest cover in the surroundings. The results suggest that replacing riparian vegetation with heterogeneous pastures, within micro-basins that lost between 30% and 60% of their forest cover, does not significantly reduce the diversity of predatory rove beetle but rather modifies the beetle composition. Effective formulation of management strategies to mitigate the impact of land use modification therefore requires an understanding of the interaction between vegetation remnants and landscape characteristics.