Trichoderma affects the physiochemical characteristics and bacterial community composition of saline–alkaline maize rhizosphere soils in the cold-region of Heilongjiang Province

Plant and Soil - Heilongjiang Province in China experiences extremely cold weather, and its soil is saline–alkaline. Salinity and alkalinity severely restrain the growth of maize. Although...     

Diversity of arbuscular mycorrhizal fungi in the rhizosphere of three host plants in the farming–pastoral zone, north China

The spatial diversity and distribution of AM fungi were investigated in three plots located in farming–pastoral zone, north China. The rhizospheres of Caragana korshinskii, Artemisia sphaerocephala and Salix psammophila were sampled and thirty AM fungal species belonging to five genera were isolated. The study demonstrated that AM fungal diversity and distribution differed significantly among the three host plants and the three studied plots. Spore density of AM fungi ranged between 2 and 22 spores per g^?1 of soil and species richness between 8 and 23. Correlation coefficient analysis demonstrated that spore density was significantly and positively correlated with soil organic matter and available N (P?<?0.01). Species richness was significantly and positively correlated with soil organic matter and available P (P?<?0.01), but significantly and negatively correlated with soil pH (P?<?0.01). Finally, the Shannon–Weiner index was significantly and positively correlated with soil organic matter (P?<?0.05). In this farming–pastoral zone, Glomus reticulatum and G.melanosporum may be more adaptable to the arid conditions than other AM fungal species. This research into AM fungal diversity may lead to exploitation of AM fungi for the mitigation of soil erosion and desertification using mycorrhizal plants, such as C.korshinskii, A.sphaerocephala and S. psammophila. The results of this study support the conclusion that diversity and distribution of AM fungi might be useful to monitor desertification and soil degradation.     

Inputs of seabird guano alter microbial growth,community composition and the phytoplankton–bacterial interactions in a coastal system

Seabird guano enters coastal waters providing bioavailable substrates for microbial plankton, but their role in marine ecosystem functioning remains poorly understood. Two concentrations of the water soluble fraction (WSF) of gull guano were added to different natural microbial communities collected in surface waters from the Ría de Vigo (NW Spain) in spring, summer, and winter. Samples were incubated with or without antibiotics (to block bacterial activity) to test whether gull guano stimulated phytoplankton and bacterial growth, caused changes in taxonomic composition, and altered phytoplankton–bacteria interactions. Alteromonadales, Sphingobacteriales, Verrucomicrobia and diatoms were generally stimulated by guano. Chlorophyll a (Chl a) concentration and bacterial abundance significantly increased after additions independently of the initial ambient nutrient concentrations. Our study demonstrates, for the first time, that the addition of guano altered the phytoplankton–bacteria interaction index from neutral (i.e. phytoplankton growth was not affected by bacterial activity) to positive (i.e. phytoplankton growth was stimulated by bacterial activity) in the low-nutrient environment occurring in spring. In contrast, when environmental nutrient concentrations were high, the interaction index changed from positive to neutral after guano additions, suggesting the presence of some secondary metabolite in the guano that is needed for phytoplankton growth, which would otherwise be supplied by bacteria.     

Evaluation of the expression stability of β-actin under bacterial infection in Macrobrachium nipponense

Molecular Biology Reports - The selection of a suitable reference gene is an important prerequisite for the precise analysis of target gene expression by real-time quantitative PCR (qPCR). The...     

Arbuscular mycorrhizal and dark septate endophytic fungi at 5,500 m on a glacier forefront in the Qinghai-Tibet Plateau, China

Arbuscular mycorrhizal (AM) and dark septate endophytic (DSE) fungi are rarely studied at extremely high elevations. Here, AM and DSE colonization in two dominant plant species (Melandrium apetalum and Poa litwinowiana) were microscopically observed on the forefront of Zhadang Glacier (5,500 m above sea level) in the Qinghai-Tibet Plateau, China. The AM fungal taxa were also identified by molecular methods. Both AM and DSE fungi synchronously colonized these two plant species, but AM dominated in M. apetalum and DSE dominated in P. litwinowiana. A total of five AM fungal spore morphotypes (Acaulospora capsicula, Diversispora sp., Glomus constrictum, G. eburneum and Glomus sp.) were found in the rhizosphere soils. Molecular identification revealed two AM fungal phylotypes: one Claroideoglomus phylotype from roots and one Diversispora phylotype from spores. These results extend the elevation at which both AM and DSE are known to occur.     

Developmental changes in β-subunit composition of Na,K-ATPase in the Drosophila eye

The Drosophila genome contains at least three loci for the Na,K-ATPase β-subunit; however, only the protein products of nrv1 and nrv2 have been characterized hitherto. Here, we provide evidence that nrv3 also encodes for a functional Na,K-ATPase β-subunit, as its protein product co-precipitates with the Na,K-ATPase α-subunit. Nrv3 expression in adult flies is restricted to the nervous system in which Nrv3 is enriched in selective types of sensory cells. Because Nrv3 expression is especially prominent in the compound eye, we have analyzed the subcellular and developmental distribution of Nrv3 within the visual cells and related this distribution to those of the α-subunit and of the β-subunits Nrv1 and Nrv2. Prospective visual cells express Nrv2 in the third larval instar stage and during the first half of pupal development. During the last third of pupal life, Nrv3 gradually replaces Nrv2 as the Na,K-ATPase β-subunit in the photoreceptor cells. Adult photoreceptors express Nrv3 as their major β-subunit; the visual cells R1–R6 co-express Nrv2 at a low level, whereas R7 and R8 co-express Nrv1. Notably, β-subunits do not co-distribute exactly with the α-subunit at some developmental stages, supporting the concept that the α-subunit and β-subunit can exist in the plasma membrane without being engaged in α/β heterodimers. The non-visual cells within the compound eye express almost exclusively Nrv2, which segregates together with the α-subunit to septate junctions throughout development.     

Starvation is associated with changes in the elemental composition of the pancreatic β-cell

By using the proton microprobe technique we have investigated the elemental composition of both pancreatic -cells and exocrine pancreas from fed and 24 h or 48 h starved obese hyperglycemic mice. Among the 15 elements measured in the -cells both Ca and Fe increased while Mg and S decreased significantly after 24 h of starvation, the effects being more pronounced after 48 h. When animals were starved for 48 h there was a decrease in the contents of Cl, Rb and Cu, whereas that of Al and Mn increased with 152 and 55%, respectively. There was an initial decrease in Na after 24 h of starvation, which was followed by an increase after 48 h. This is in contrast to Cd, which first increased and then decreased to a value lower than that obtained in the fed animal. The content of K showed a small decrease and that of Pb showed an increase only in the 24 h starved group. In the -cells the contents of Zn and P did not change subsequent to starvation. In the exocrine pancreas Na, Cl and P decreased after 24 h of starvation and except for Na, the decrease was maintained when the starvation period was increased to 48 h. After 24 h there was a significant, though transient, increase in K, Mg and Rb. With regard to the contents of Zn, Cu and S there was a progressive decrease as the starvation continued. In contrast to the endocrine pancreas the content of Al in the exocrine pancreas did not change after 48 h of starvation. There was no change in islet insulin content subsequent to starvation. The extent to which the observed changes in -cell elemental composition is involved in the impaired insulin release associated with starvation, merits further investigations.     

Symmetry-related mutants in the quinone binding sites of the bacterial reaction center – the effects of changes in charge distribution

To probe the structural elements that contribute to the functional asymmetries of the two ubiquinone₁₀ binding pockets in the reaction center of Rhodobacter capsulatus, we targeted the L212Glu–L213Asp (near Q_B) and the M246Ala-M247Ala (near Q_A) pairs of symmetry-related residues for site-specific mutagenesis. We have constructed site-specific mutants that eliminate the sequence differences at these positions (L212Glu–L213AspAla-Ala or M246Ala–M247AlaGlu-Asp), and have reversed that asymmetry by constructing a quadruple-mutant strain, RQ (L212Glu–L213Asp-M246Ala–M247AlaAla-Ala-Gl u-Asp). The mutations were designed to change the charge distribution in the quinone-binding region of the reaction center; none of the strains is capable of photosynthetic growth. In photocompetent phenotypic revertants of the RQ strain, second-site mutations which affect Q_B function are coupled to mutations in the Q_A site which restore an Ala or substitute a Tyr at the M247 site; one strain carries an additional MetLeu substitution at M260 near Q_A. All of the RQ revertants retain the engineered M246AlaGlu mutation in the Q_A site as well as the L212Ala–L213Ala mutations in the Q_B site. Kinetic characterization of the RQ revertants will give us an idea of what structural and functional elements are important for restoring efficiency to electron and proton transfer pathways in the RQ RC, which is far from native. To date, these preliminary results underscore the importance of an asymmetric distribution of polar amino acids in the quinone binding pockets and its influence on the functional properties of the reaction center.     

Ciliate food vacuole content and bacterial community composition in the warm-monomictic crater Lake Alchichica, México

To evaluate trophic relationships between ciliates and bacterioplankton during the stratification period in a lake, samples from three different layers [the upper part of the metalimnion (UM), the base of the metalimnion (BM) and the hypolimnion] were studied. The autotrophic picoplankton numbers, phylogenetic composition of heterotrophic picoplankton (HPP), and HPP composition in ciliates' food vacuoles were analyzed. Additionally, in situ incubations in dialysis bags were performed at the same selected depths to assess potential changes in picoplankton composition related to ciliates' feeding activity. Among the in situ HPP assemblage, no phylogenetic group dominated in the selected layers within the course of the study. The ciliate assemblage was dominated by scuticociliates, haptorids, and hypotrichs. Comparing ciliates' food vacuole content and in situ HPP composition, a high preference for Alphaproteobacteria was found at all three depths. Planctomycetes, and Delta- and Gammaproteobacteria were selected at BM and hypolimnion, respectively. However, selection of a given phylogenetic group in the time course of this study was observed only for Alphaproteobacteria in the UM. Similar trends were found in the incubations, but no relationship was found between the vacuole content of the ciliates and changes in HPP composition.     

Analysis of bacterial communities on aging flue-cured tobacco leaves by 16S rDNA PCR–DGGE technology

Many microorganisms, growing on aging flue-cured tobacco leaves, play a part in its fermentation process. These microflora were identified and described by culture-dependent methods earlier. In this study we report the identity of the microflora growing on the tobacco leaf surface by employing culture-independent methods. We have amplified microbial 16S rDNA sequences directly from the leaf surface and used denaturing gradient gel electrophoresis (DGGE) to identify bacterial community on the tobacco leaves. Our culture-independent methods for the study of microbial community on tobacco leaves showed that microbial community structures on leaves of variety Zhongyan 100, NC89 and Zhongyan 101 were similar between 0 and 6 months aging, and between 9 and 12 months aging, while the similarity is low between 0 and 6, and between 9 and 12 months aging, respectively. There were certain similarities of bacterial communities (similarity up to 63%) among the three tobacco varieties for 0 to 6 months aging. Five dominant 16S rDNA DGGE bands A, B, C, D and E were isolated, cloned, and sequenced. They were most similar to two cultured microbial species Bacteriovorax sp. EPC3, Bacillus megaterium, and three uncultured microbial species, respectively.     

Changes in the bacterial community in the fermentation process of kôso,a Japanese sugar-vegetable fermented beverage

Kôso is a Japanese fermented beverage made with over 20 kinds of vegetables, mushrooms, and sugars. The changes in the bacterial population of kôso during fermentation at 25 °C over a period of 10 days were studied using 454 pyrosequencing of the 16S rRNA gene. The analysis detected 224 operational taxonomic units (OTUs) clustered from 8 DNA samples collected on days 0, 3, 7, and 10 from two fermentation batches. Proteobacteria were the dominant phylum in the starting community, but were replaced by Firmicutes within three days. Seventy-eight genera were identified from the 224 OTUs, in which Bifidobacterium, Leuconostoc, Lactococcus, and Lactobacillus dominated, accounting for over 96% of the total bacterial population after three days’ fermentation. UniFrac–Principal Coordinate Analysis of longitudinal fermented samples revealed dramatic changes in the bacterial community in kôso, resulting in significantly low diversity at the end of fermentation as compared with the complex starting community.     

Participation of algal–bacterial community in the formation of modern stromatolites in Cock Soda Lake,Altai Region

Modern dolomite stromatolites are found in Cock Soda Lake (Kulunda Steppe) at a salinity of 100–200 g/L and pH of 10. The mineralogical analysis has revealed the presence in the stromatolites of Ca?Mg-carbonates of various compositions. The organisms–edificators of the phototrophic community developing in the lake are determined. They are identified as a part of the mineralized biota (cyanobacteria, bacteria, and eukaryotic alga Ctenocladus circinnatus). Morphological and ultrastructural features of exopolysaccharides secreted by cyanobacteria and bacteria dominant in the phototrophic community are characterized. It is shown that polysaccharides secreted primarily by cyanobacteria have the utmost importance for the formation of stromatolites in Petukhovskoe Soda Lake.     

Dominance of Lysobacter sp. in the rhizosphere of two coastal sand dune plant species, Calystegia soldanella and Elymus mollis

Bacterial diversity in the rhizosphere of beach morning glory (Calystegia soldanella) and wild rye (Elymus mollis), two of the major plant species inhabiting the coastal sane dune in Tae-An, Korea, was studied by the analysis of community 16S rRNA gene clones. The amplified rDNA restriction analysis (ARDRA) of the clones using HaeIII exhibited significant differences in the community composition between the two plant species as well as regional differences, but also identified a specific ARDRA pattern that was most common among the clones regardless of plant species. Subsequent sequence analysis indicated that the pattern was that of Lysobacter spp., which is a member of the family Xanthomonadaceae, class Gamma proteobacteria. The Lysobacter clones comprised 50.6% of the clones derived from C. soldanella and 62.5% of those from E. mollis. Other minor patterns included those of Pseudomonas spp., species of Rhizobium, Chryseobacterium spp. and Pantoea spp. among C. soldanella clones, and Pseudomonas sp. and Aeromonas hydrophila among E. mollis clones. It is not yet clear what kind of roles Lysobacter plays in association with sand dune plants, but its universal presence in the rhizosphere, together with the potential of this taxon for antagonistic activity against plant pathogens, suggests that Lysobacter might form a symbiotic relationship with its host plants.     

Plant community composition and structural characteristics of an invaded forest in the Galápagos

Non-native species have invaded habitats worldwide, greatly impacting the structure and function of native communities and ecosystems. To better understand mechanisms of invasion impacts and how to restore highly impacted and transformed ecosystems, studies are needed that evaluate invader effects on both biotic communities and structural characteristics. On Santa Cruz Island in Galápagos we compared biotic (plant species richness, diversity, and community composition) and structural (canopy openness, forest height, and leaf litter) characteristics of a relic forest dominated by an endemic and highly threatened tree and a forest dominated by an invasive tree. The forests are located within the historical distribution of the endemic tree, which now occupies only 1% of its original extent. We found that the invaded forest had 42% lower native plant species richness and 17% less plant diversity than the endemic tree dominated forest. Additionally, with the invader there was 36% greater non-native plant species richness, 37% higher non-native plant diversity, and highly dissimilar plant composition when compared to the endemic-dominated forest. Additionally, the invaded forest had a more open and taller tree canopy and greater leaf litter cover than native forest. The presence of the invasive tree and the associated forest structural changes were the primary factors in models that best explained higher non-native diversity in the invaded forest. Our correlational results suggest that an invasive tree has significantly altered plant assemblage and forest structural characteristics in this unique ecosystem. Experiments that remove the invader and evaluate native plant community responses are needed to identify thresholds for practical restoration of this threatened and biologically unique native forest.     

Microbial community composition of anoxic marine sediments in the Bay of Cádiz (Spain)

The composition of the microbial community inhabiting the anoxic coastal sediments of the Bay of Cádiz (southern Spain) was investigated using a molecular approach consisting of PCR cloning and denaturing gradient gel electrophoresis (DGGE), based on 16S rRNA sequences. The total cell count was 1-5 × 10? cells/g sediment and, as determined by catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH), the proportion of Bacteria to Archaea was about 70:30. The analysis of 16S-rRNA gene sequences revealed a wide spectrum of microorganisms, which could be grouped into 111 operational taxonomic units (OTUs). Many of the OTUs showed high phylogenetic similarity to microorganisms living in marine sediments of diverse geographic origin. The phylogenetic groups that were predominantly detected were Firmicutes, Deltaproteobacteria, and Gammaproteobacteria, accounting for 23, 15, and 14% of the clones, respectively. Diversity in the domain Archaea was significantly lower than in the domain Bacteria. The majority of the archaeal OTUs belonged to the Crenarchaeota phylum. Since most of the sequences could not be identified precisely at the genus/species level, the functional roles of the microorganisms in the ecosystem could not be inferred. However, seven OTUs affiliated with the Delta- and Epsilonproteobacteria were identified down to the genus level, with all of the identified genera known to occur in sulfate-rich marine environments.