Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor

Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system.     

Gelatin filter capture-based high-throughput sequencing analysis of microbial diversity in haze particulate matter

Airborne particulate matter (PM), especially PM_2.5, can be easily adsorbed by human respiratory system. Their roles in carrying pathogens for spreading epidemic diseases has attracted great concern. Herein, we developed a novel gelatin filter-based and culture-independent method for investigation of the microbial diversity in PM samples during a haze episode in Tianjin, China. This method involves particle capture by gelatin filters, filter dissolution for DNA extraction, and high-throughput sequencing for analysis of the microbial diversity. A total of 584 operational taxonomic units (OTUs) of bacteria and 370 OTUs of fungi at the genus level were identified during hazy days. The results showed that both bacterial and fungal diversities could be evaluated by this method. This study provides a convenient strategy for investigation of microbial biodiversity in haze, facilitating accurate evaluation of airborne epidemic diseases.     

Structural differentiation of bacterial communities in indole-degrading bioreactors under denitrifying and sulfate-reducing conditions

The acclimated, anaerobic microbial community is an efficient method for indole-containing wastewater treatment. However, our understanding of the diversity of indole-degrading communities is still limited. We investigated two anaerobic, indole-decomposing microbial communities under both denitrifying and sulfate-reducing conditions. Utilizing a near full-length 16S rRNA gene clone library, the most dominant bacteria in the denitrifying bioreactor identified was β-proteobacteria. Among these, bacteria from genera Alicycliphilus, Acaligenes and Thauera were abundant and thought responsible for indole degradation. However, in the sulfate-reducing bioreactor, Clostridia and Actinobacteria were the dominant bacterial class found and likely the main degrading species. Microbial communities in these bioreactors shared only two operational taxonomic units (OTUs). Differences in the electron acceptors of denitrification or sulfate reduction may be responsible for the higher indole removal capacity in the denitrifying bioreactor (80%) than the capacity in the sulfate-reducing bioreactor (52%). This study is the first detailed analysis of an anaerobic indole-degrading community.     

Species diversity of culturable endophytic fungi from Brazilian mangrove forests

This study aimed to perform a comparative analysis of the diversity of endophytic fungal communities isolated from the leaves and branches of Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa trees inhabiting two mangroves in the state of São Paulo, Brazil [Cananeia and Bertioga (oil spill-affected and unaffected)] in the summer and winter. Three hundred and forty-three fungi were identified by sequencing the ITS1-5.8S-ITS2 region of rDNA. Differences were observed in the frequencies of fungi isolated from the leaves and branches of these three different plant species sampled from the Bertioga oil spill-affected and the oil-unaffected mangrove sites in the summer and winter; these differences indicate a potential impact on fungal diversity in the study area due to the oil spill. The molecular identification of the fungi showed that the fungal community associated with these mangroves is composed of at least 34 different genera, the most frequent of which were Diaporthe, Colletotrichum, Fusarium, Trichoderma and Xylaria. The Shannon and the Chao1 indices [H′_(95 %) = 4.00, H′_(97 %) = 4.22, Chao1_(95 %) = 204 and Chao1_(97 %) = 603] indicated that the mangrove fungal community possesses a vast diversity and richness of endophytic fungi. The data generated in this study revealed a large reservoir of fungal genetic diversity inhabiting these Brazilian mangrove forests and highlighted substantial differences between the fungal communities associated with distinct plant tissues, plant species, impacted sites and sampling seasons.     

An amalgam of pathogenic and beneficial endophytic fungi colonizing four Dendrobium species from Meghalaya,India

Endophytic fungi are known to play an important role in driving the evolution of plants by conferring adaptational advantages to their host through the production of secondary metabolites and phytohormones. In this study, we evaluated the diversity and phylogenetic relationship of endophytic fungal communities from four Dendrobium species viz., Dendrobium chrysanthum, Dendrobium heterocarpum, Dendrobium hookerianum, and Dendrobium longicornu of Meghalaya, India. A total of 51 culturable endophytic fungi were isolated from the four selected orchid species. The isolates were identified based on nuclear large subunit sequences into 33 species. Approximately 91% of the isolates showed affinity to Ascomycetes, while 9% of the isolates showed BLAST search similarity to Basidiomycetes. The most common genera were Trichoderma and Xylaria. The most prevalent genera were Fusarium, which was detected in all the four Dendrobium species followed by Diaporthe, which was present in three Dendrobium species viz., D. chrysanthum, D. hookerianum, and D. heterocarpum. The Shannon index value of endophytic fungal communities was the highest in D. chrysanthum (2.66), while D. longicornu (1) had the highest Evenness index. The present study revealed that endophytic fungi in these orchids are an amalgam of pathogenic and beneficial fungi, which have, at the least, switched their lifestyle to asymptomatic endophyte in their host. To our knowledge, this is the first such report on the diversity of endophytic fungi in the four selected Dendrobium species from Meghalaya, India.     

Study on the correlation between soil microbial diversity and ambient environmental factors influencing the safflower distribution in Xinjiang

The effects of soil microbial properties and physiographical factors on safflower distributions in the main safflower plantations of Xinjiang province in China were studied. This study may help determine the basis of the environmental factors for evaluating the geoherbalism of this medicinal plant. The soil microbial biodiversity in the bulk soil and rhizosphere of safflower at different growth stages and from different sampling plots were characterized by analyzing the environmental DNAs in the samples. With general primers targeting the 16S ribosomal DNA for bacteria and the internal transcribed spacer 1 gene for fungi, the study was performed using marker gene amplification coupled with Illumina HiSeq high-throughput sequencing technologies. Correlation analysis and a distance-based redundancy analysis were performed to determine the dominant factors affecting the distribution of the microorganism in safflower soils. A total of 16517 bacterial operational taxonomic units (OTUs) were obtained from all the 108 soil samples of nine safflower sampling plots. At the phylum level, 48 phyla have been identified with Actinobacteria (32.9%) and proteobacteria (28.7%) being predominant. For fungi, 8746 OTUs were obtained, which belonged to seven phyla with Ascomycota overwhelmingly superior in relative abundance. A significant positive correlation was found between soil microbe quantity and ASL (above sea level). Safflower was sensitive to changes in elevation, growing more abundantly in the mountainous regions at heights of around 1,200 m above sea level. It is concluded that the dominant factors affecting the distribution of microorganisms in safflower soils were soil moisture, available N, and ASL.     

Effects of pH on the comparative culturability of fungi and bacteria from acidic and less acidic forest soils

Under aerobic conditions, the culturable microbial population of acidic forest soils was more tolerant to acidic cultivation conditions than was the culturable microbial population of less acidic soils. The number of culturable bacteria decreased sharply under acidic cultivation conditions, while the number of culturable fungi remained relatively constant over the pH range 2.2–6.5. The ratios of culturable bacteria to culturable fungi were greater than one at pH 6.5; in contrast, the bacteria-to-fungi ratios were less than one at pH 2.2–4. At pH's approximating those of the soils examined, culturable fungi predominated the culturable microbial community in acidic soils. However, relative to the populations resolved, acidic forest soils displayed a more acid tolerant bacterial population than did less acidic forest soils. The culturable fungal population contained both filamentous and yeast morphologies. An acid-tolerant fungal isolate that grew at pH 1 was identified as a subspecies of Penicillium frequentans, and an acid-tolerant yeast that grew at pH 2 was identified as the yeast stage of the basidiomycetes Ustilago maydis.     

Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils

The microbial community (bacterial, archaeal, and fungi) and eight genes involved in the nitrogen biogeochemical cycle (nifH, nitrogen fixation; bacterial and archaeal amoA, ammonia oxidation; narG, nitrate reduction; nirS, nirK, nitrite reduction; norB, nitric oxide reduction; and nosZ, nitrous oxide reduction) were quantitatively assessed in this study, via real-time PCR with DNA extracted from three Antarctic soils. Interestingly, AOB amoA was found to be more abundant than AOA amoA in Antarctic soils. The results of microcosm studies revealed that the fungal and archaeal communities were diminished in response to warming temperatures (10 °C) and that the archaeal community was less sensitive to nitrogen addition, which suggests that those two communities are well-adapted to colder temperatures. AOA amoA and norB genes were reduced with warming temperatures. The abundance of only the nifH and nirK genes increased with both warming and the addition of nitrogen. NirS-type denitrifying bacteria outnumbered NirK-type denitrifiers regardless of the treatment used. Interestingly, dramatic increases in both NirS and NirK-types denitrifiers were observed with nitrogen addition. NirK types increase with warming, but NirS-type denitrifiers tend to be less sensitive to warming. Our findings indicated that the Antarctic microbial nitrogen cycle could be dramatically altered by temperature and nitrogen, and that warming may be detrimental to the ammonia-oxidizing archaeal community. To the best of our knowledge, this is the first report to investigate genes associated with each process of the nitrogen biogeochemical cycle in an Antarctic terrestrial soil environment.     

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM > M > S > DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation.     

Arbuscular mycorrhizal fungi serve as keystone taxa for revegetation on the Tibetan Plateau

Revegetation is widely used to enhance degraded topsoil recovery with the enhancements of soil nutrient accumulation and soil structure stabilization. Arbuscular mycorrhizal fungi (AMF) are important for the allocation of carbon into the soil and the formation of soil aggregates. Thus, we hypothesized that AMF could construct more niches for other microbes during revegetation, making AMF keystone taxa of soil. Soil fungal and bacterial communities were investigated under a revegetation experiment and correlation networks between soil fungi and bacteria were constructed. Simultaneously, the plant growth level, soil properties and structure, and soil microbial carbon decomposition abilities were measured. The results revealed that AMF were the most central fungi at the phylum (degree = 3), class (degree = 11), and family (degree = 15) levels. The reads number of AMF were positively correlated with both fungal (R² = 0.431, P < 0.001) and bacterial (R² = 0.106, P = 0.044) richness. Higher colonization of AMF in roots and/or more AMF extraradical mycelium and spores in soil indicated a better plant growth, more stable soil aggregates, and a higher carbon decomposition ratio. Our results highlight that AMF are keystone taxa in revegetation, as they play significant roles in enhancing the recovery of the belowground microbiome diversity, soil structure stability, and nutrients cycling. The positive roles of AMF in revegetation support the application of AMF in ecosystem recovery.     

Endophytic colonization of entomopathogenic fungi increases plant disease resistance by changing the endophytic bacterial community

Various mechanisms are involved in plant disease resistance mediated by entomopathogenic fungi; however, the role of plant endophytic microbes in disease resistance is unknown. In the present study, we showed that the disease incidence of northern corn leaf blight caused by Exserohilum turcicum (Et) on maize was reduced significantly by soil inoculation with Beauveria bassiana (Bb). Meanwhile, B. bassiana colonization and E. turcicum infection increased the diversity and abundance and diversity of endophytic bacteria and fungi, respectively, while the abundance of endophytic bacterial of the Bb + Et treatment decreased significantly compared with that of Et treatment alone. However, Bb + Et treatment increased the relative abundance of plant beneficial bacteria significantly, for example, Burkholderia and Pseudomonas. Network analyses showed that the microbiome complexity increased after soil inoculation with B. bassiana. Taken together, these results revealed the potential mechanism by which entomopathogenic fungi exert biological control of maize leaf spot disease.     

Fungal endophytes in five medicinal plant species from Kudremukh Range, Western Ghats of India

Eighteen species of endophytic fungi were isolated from bark, stem and leaf segments of five medicinal plant species growing within the Kudremukh range in the Western Ghats of India. The dominant endophytic fungal species isolated from these plant species were Curvularia clavata, C. lunata, C. pallescens and Fusarium oxysporum. The highest species richness as well as frequency of colonization of endophytic fungi was found in the leaf segments, rather than the stem and bark segments, of the host plant species. The greatest number of endophytic fungal species were found within Callicarpa tomentosa (11 species), whereas Lobelia nicotinifolia harbored the lowest number of fungal endophytes (5 species). This study provides evidence that fungal endophytes are host and tissue specific.     

Particle‐attached microorganism oxidation of ammonia in a hypereutrophic urban river

To elucidate the importance and mechanisms of particle‐attached microorganisms on ammonia oxidation, we conducted a controlled simulation experiment with samples collected from the Shunao River, an ammonia‐rich hypereutrophic urban river in eastern China. The effects of particle concentration, ammonia concentration, organic carbon source and concentration, dissolved oxygen concentration, and pH were investigated on ammonia transformation rate (ammonia removal rate and NO₂^? + NO₃^? accumulation rate) and abundance of particle‐attached ammonia‐oxidizing bacteria (AOB) and archaea (AOA). All these factors significantly influenced ammonia transformation rates. Our results provided direct evidence that microorganisms attached on riverine suspended particles were associated with ammonia oxidation. Sequencing revealed that the AOA genus Nitrososphaera, and the AOB genus Nitrosomonas were the most dominant in particle‐attached ammonia‐oxidizing microbial communities. Further analysis showed that AOB communities had higher species richness and diversity compared with AOA communities. Additionally, AOB amoA genes were ~10–100 times more abundant than AOA amoA genes, and AOB abundance was more strongly correlated with ammonia transformation rates than AOA abundance in most experiments, indicating that particle‐attached AOB were more important than AOA in the hypereutrophic urban river. This study adds to our knowledge of particle‐attached microorganism oxidation of ammonia.     

Diversity of arbuscular mycorrhizal fungi associated with acacia trees in southwestern Saudi Arabia

Acacia species produce extensive, deep root systems with a capacity to develop mycorrhizal symbioses that facilitate plant nutrition via enhanced soil nutrient absorption. This study aimed to evaluate the mycorrhizal status and the diversity of arbuscular mycorrhizal fungi (AMF) associated with acacia trees in southwestern Saudi Arabia. The mycorrhizal status varied greatly between species. The highest values of AMF root colonization and spore density were observed in the roots and in the rhizospheric soil of Acacia negrii. DNA was extracted from plant roots and the AMF large subunit ribosomal DNA (LSU rDNA) was amplified by a nested polymerase chain reaction. A total of 274 LSU rDNA cloned fragments from roots of the three acacia trees were sequenced. Phylogenetic analysis revealed a high AMF diversity, especially in Acacia tortilis. On the basis of LSU rDNA sequences, AMF was grouped into five genera: Glomus, Claroideoglomus, Acaulospora, Gigaspora, and Scutellospora. The genus Glomus fungi were the dominant colonizers of all three acacia species, while the genus Scutellospora fungi were found only in A. tortilis roots. The high AMF-acacia diversity suggests that AMF plays an important role in the sustainability of acacia species in the arid environment.     

Structural diversity and efficacy of culturable cellulose decomposing bacteria isolated from rice–pulse resource conservation practices

The diversity of cellulolytic bacteria from the rice–pulse system can be sourced for identification of efficient cellulose decomposing microbial strains. In the present study, the abundance, structural diversity, and cellulolytic potential of the culturable bacterial community were studied in 5‐year old rice–pulse system under different resource conservation technologies. Higher cellulose (68% more) and xylanase (35% more) activities were observed under zero tilled soil. The populations of cellulolytic bacteria were significantly higher (44%) in zero tillage (ZT) treatment than those of conventional practice. Results revealed that the cellulolytic bacterial diversity was found to be significantly higher under ZT practice, but the present population may not be sufficient for effective recycling of organic wastes in this system. Out of 290 bacterial isolates, 20 isolates had significantly higher cellulolytic activities, of which the top three superior isolates were received from ZT practice. The cellulolytic bacterial diversity based on 16S rDNA sequencing data revealed that the Firmicutes was the most dominant phyla and the Bacillus spp. were the common genus, the observation also showed that there were 17 different haplotypes were recorded among 20 isolates of cellulolytic bacteria. The present findings indicated that long‐term ZT in the rice–pulse system could be a unique source for efficient cellulose decomposing bacteria and further the efficient bacterial strains isolated from this system can be used as efficient bioinoculants for in situ as well as ex‐situ decomposition of rice straw particularly in conservation agriculture.     

Endophytic bacterial diversity in roots of Typha angustifolia L. in the constructed Beijing Cuihu Wetland (China)

We investigated the community structure of endophytic bacteria in narrowleaf cattail (Typha angustifolia L.) roots growing in the Beijing Cuihu Wetland, China, using the 16S rDNA library technique. In total, 184 individual sequences were used to assess the diversity of endophytic bacteria. Phylogenetic analysis revealed that 161 clones (87.5%) were affiliated with Proteobacteria, other clones grouped into Cytophaga/Flexibacter/Bacteroids (3.3%), Fusobacteria (3.8%), and nearly 5% were uncultured bacteria. In Proteobacteria, the beta and gamma subgroups were the most abundant, accounting for approximately 46% and 36.6% of all Proteobacteria, respectively. The dominant genera included Rhodoferax, Pelomonas, Uliginosibacterium, Pseudomonas, Aeromonas, Rhizobium, Sulfurospirillum, Ilyobacter and Bacteroides. While some of these endophytic bacteria are capable of fixing nitrogen and can therefore improve plant growth, other endophytes may play important biological roles by removing nitrogen, phosphorus and/or organic matter from the water body and thus have the potential to enhance the phytoremediation of eutrophic water bodies. These bacteria have the potential to degrade xenobiota such as methane, methanol, methylated amines, catechol, oxochlorate, urea, cyanide, and 2,4-dichlorophenol. Hence, the use of certain endophytic bacteria in the process of phytoremediation could be a powerful approach for the restoration of eutrophic systems.     

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2–6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at <pH 3 described in the literature.     

Fungal recovery and characterization from Hindu Kush mountain range,Tirich Mir glacier,and their potential for biotechnological applications

The Hindu Kush mountains spread over Northern areas of Pakistan having hundreds of glaciers representing a unique ecosystem driven by the specific geochemistry and climate. The current study measured the distribution of culturable fungi in Tirich Mir glacier, Hindu Kush range, and the potential of these isolates to show antimicrobial activity and produce biotechnologically important enzymes. Samples of glacial ice, sediments, and meltwater were collected from Tirich Mir glacier, and 46 fungal strains were isolated and characterized for identity and biotechnological applications. The findings revealed Penicillium (10) as the most common genus, followed by Alternaria (9), Cladosporium (7), Coprinopsis, two isolates each belonging to genus Phoma, Ulocladium, Epicoccum, Onygenales, and Didymella, and one isolate of genus Davidiella, Aspergillus, Geomyces, Dothideomycetes, Pseudogymnoascus, Irpex, Scopulariopsis, Ascochyta, Tomicus, and Davidiellaceae. Davidiella tassiana HTF9 showed growth in the presence of 18% NaCl and pH 2, 3, 5, 7, 9, and 11. The isolates Ulocladium sp. and Onygenales sp. inhibited the growth of test fungi, Gram-negative and positive bacteria. Fungal strains were capable of producing cold-active enzymes, including cellulase, lipase, amylase, and deoxyribonuclease. The isolate Penicillium chrysogenum HTF24 was an efficient producer of amylase, deoxyribonuclease, and cellulase. The fungi of high-altitude glaciers are potent candidates for biotechnological applications; however, studies using more sensitive techniques are needed for further exploration.     

Genetic differentiation and phylogenetic potential of Ty3/Gypsy LTR retrotransposon markers in soil and plant pathogenic fungi

Genetic diversity studies are crucial for understanding the genetic structure and evolutionary dynamics of fungal species and communities. Fungal genomes are often reshaped by their repetitive components such as transposable elements. These elements are key players in genomic rearrangements and are ideal targets for genetic diversity and evolutionary studies. Herein, we used three Ty3/Gypsy long terminal repeat retrotransposons, Grasshopper, Maggy, and Pyret, for genetic differentiation and diversity in soil and plant pathogenic fungi, representing diverse species, order, and phyla. Pyret DNA markers showed the highest gene diversity and Shannon's information indices, followed by Maggy and Grasshopper. The observed high levels of multilocus polymorphism indicate the continuous mobility of these elements after their transfer in the new host. In conclusion, this study presents novel markers for genetic differentiation and evolutionary studies of fungi, and sheds light on the prevalence of gene acquisition phenomenon in field fungi.