Impacts of cultivation of marine diatoms on the associated bacterial community

The composition of bacterial communities associated with four diatom species was monitored during isolation and cultivation of algal cells. Strong shifts in the associated communities, linked with an increase in the numbers of phylotypes belonging to members of the Gammaproteobacteria, were observed during cultivation.     

Ectomycorrhizal fungal communities in Nothofagus nervosa (Raulí): A comparison between domesticated and naturally established specimens in a native forest of Patagonia,Argentina

Due to its overexploitation during the past century, Nothofagus nervosa is currently included in conservation and domestication programs, in which ectomycorrhizas play an important role. We aimed to describe the abundance and diversity of ectomycorrhizal fungi (EcMF) in both domesticated and naturally established N. nervosa specimens, and to analyse the influence of age, seasonality and forest management on EcMF communities. The occurrence of arbuscular mycorrhizas (AM) and dark septate endophytes (DSE) was also investigated. Fungal diversity and taxonomic identification were assessed by morphotyping and subsequent ITS-rDNA sequencing. Plant age, seasonality and forest management influenced EcMF communities. Colonization rates were higher than 90 % in all the specimens, and were significantly higher in mature trees and in autumn. The highest EcMF richness and diversity values were registered in domesticated specimens and in autumn. Most EcMF were basidiomycetes, belonging mainly to the Cortinariaceae and Tricholomataceae. Arbuscular mycorrhizas were not detected, while DSE were present within N. nervosa roots. Our results and previously published reports showed that some EcMF are capable of colonizing different Nothofagus species. In addition, the EcMF described in natural ecosystems are different from those colonizing N. nervosa during its cultivation in the nursery. These results improve our understanding of key factors affecting EcMF communities associated with Nothofagus in native forests and nurseries (age, season, forest management, cultivation techniques), and this information is relevant for improving domestication programs.     

Effect of Cry1Ab protein on rhizobacterial communities of Bt-maize over a four-year cultivation period

Background

Bt-maize is a transgenic variety of maize expressing the Cry toxin from Bacillus turingiensis. The potential accumulation of the relative effect of the transgenic modification and the cry toxin on the rhizobacterial communities of Bt-maize has been monitored over a period of four years.

Methodology/Principal Findings

The accumulative effects of the cultivation of this transgenic plant have been monitored by means of high throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region from rhizobacterial communities. The obtained sequences were subjected to taxonomic, phylogenetic and taxonomic-independent diversity studies. The results obtained were consistent, indicating that variations detected in the rhizobacterial community structure were possibly due to climatic factors rather than to the presence of the Bt-gene. No variations were observed in the diversity estimates between non-Bt and Bt-maize.

Conclusions/Significance

The cultivation of Bt-maize during the four-year period did not change the maize rhizobacterial communities when compared to those of the non-Bt maize. This is the first study to be conducted with Bt-maize during such a long cultivation period and the first evaluation of rhizobacterial communities to be performed in this transgenic plant using Next Generation Sequencing.     

Changes in Bacterial Communities of the Marine Sponge Mycale laxissima on Transfer into Aquaculture

The changes in bacterial communities associated with the marine sponge Mycale laxissima on transfer to aquaculture were studied using culture-based and molecular techniques. M. laxissima was maintained alive in flowthrough and closed recirculating aquaculture systems for 2 years and 1 year, respectively. The bacterial communities associated with wild and aquacultured sponges, as well as the surrounding water, were assessed using 16S rRNA gene clone library analysis and denaturing gradient gel electrophoresis (DGGE). Bacterial richness and diversity were measured using DOTUR computer software, and clone libraries were compared using S-LIBSHUFF. DGGE analysis revealed that the diversity of the bacterial community of M. laxissima increased when sponges were maintained in aquaculture and that bacterial communities associated with wild and aquacultured M. laxissima were markedly different than those of the corresponding surrounding water. Clone libraries of bacterial 16S rRNA from sponges confirmed that the bacterial communities changed during aquaculture. These communities were significantly different than those of seawater and aquarium water. The diversity of bacterial communities associated with M. laxissima increased significantly in aquaculture. Our work shows that it is important to monitor changes in bacterial communities when examining the feasibility of growing sponges in aquaculture systems because these communities may change. This could have implications for the health of sponges or for the production of bioactive compounds by sponges in cases where these compounds are produced by symbiotic bacteria rather than by the sponges themselves.     

Did alder (Alnus) fires trigger rice cultivation in the lower reaches of the Yangtze River,East China?

It remains debatable as to how the prehistoric human communities managed the environment to enable the initial cultivation of rice during the early Neolithic in the coastal lower reaches of the Yangtze River, East China. Previous studies proposed an environmental context for the first rice cultivation at Kuahuqiao, Hangzhou, based on an archaeological sedimentary microfossil record that had been well-dated using radiocarbon methods. Those studies suggested that early humans began burning the predominantly alder scrub in a local swampy wetland, starting about 7750 cal. yr BP, which permitted the start of dedicated rice (Oryza) cultivation. Here we present a new, finer-detailed pollen-phytolith-microscopic charcoal record from the same locality. Our result reveals that local woods dominated by oak (Quercus) and pine (Pinus) were targeted for burning by early cultivators before the start of rice agriculture.     

The role of in vitro cultivation on asymbiotic trait variation in a single species of arbuscular mycorrhizal fungus

Cultivating arbuscular mycorrhizal (AM) fungi in vitro is an efficient way to produce material for industry and research. However, such artificial growing conditions may impose selective pressure on fungi grown in vitro over many generations. We hypothesized that isolates subjected to long term propagation in vitro may develop increasingly ruderal traits. We proposed a predictive framework for the effect of in vitro cultivation on asymbiotic AM fungal traits. Using photomicrography and image processing, we analyzed morphology and growth traits for 14 isolates representing an in vitro cultivation gradient from 0 to >80 generations in vitro. We investigated the range of trait variation among asymbiotic growth of arbuscular mycorrhizal (AM) fungus isolates (Rhizoglomus irregulare). Spore dormancy was strongly associated with in vitro cultivation. We observed extremely high levels of inter-isolate variation for most fungal traits, but this was not related to time in vitro. Our results indicate that intra-specific diversity may have a strong ecological role in AM fungal communities.     

Occurrence of Pasteuria-like Organisms on Selected Plant-Pamsitic Nematodes of Pineapple in the Hawaiian Islands

Soils from 320 sites representing diverse undisturbed habitats from five Hawaiian Islands were assessed for occurrence of Pasteuria-like organisms. Mean annual rainfall at sites ranged from 125-350 cm, elevation from 69-2,286 m, and annual mean temperature from 12-24 C. Seven different natural communities were represented: wet lowland, mesic lowland, wet montane, mesk montane, dry montane, mesic subalpine, and dry alpine. Pasteuria spp. in a soil sample was detected by baiting with infective stages of Helicotylenchus dihystera, Meloidogyne javanica, Pratylenchus brachyurus, and Rotylenchulus reniformis, followed by cultivation of the nematodes on pineapple plants for 10-11 months. All nematode baits except R. reniformis were readily recovered from the soil samples. A sample was considered Pasteuria-positive if at least 5 % of the nematode specimens showed endospore attachment. Thirteen percent of all samples were positive for Pasteuria-like organisms. The frequencies of association between Pasteuria spp. and Meloidogyne, Helicotylenchus, or Pratylenchus species were 52%, 24%, and 24%, respectively. Positive samples were more prevalent on the older islands of Kauai and Oahu (75%), in lowland communities (61%), and in areas with introduced vegetation (60%). More than 27% of the positive samples were associated with plant species in a few selected families that included Meliaceae and Myrtaceae. Occurrence of Pasteuria spp. seemed to be positively associated with mean annual rainfall or temperature, but negatively associated with elevation.     

Fungal diversity in galls of baldcypress trees

The baldcypress midge (Taxodiomyia cupressi and Taxodiomyia cupressiananassa) forms a gall that originates from leaf tissue. Female insects may inoculate galls with fungi during oviposition, or endophytes from the leaf tissue may grow into the gall interior. We investigated fungal diversity inside of baldcypress galls, comparing the gall communities to leaves and comparing fungal communities in galls that had successful emergence versus no emergence of midges or parasitoids. Galls of midges that successfully emerged were associated with diverse gall fungal communities, some of which were the same as the fungi found in surrounding leaves. Galls with no insect emergence were characterized by relatively low fungal diversity.     

Application of terminal restriction fragment length polymorphism (T-RFLP) analysis to monitor effect of biocontrol agents on rhizosphere microbial community of hot pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.)

Microbial communities in hot pepper (Capsicum annuum L.) cultivation fields under different cultivation methods were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis. Rhizosphere soil and leaf samples were collected from control, conventional and nature-friendly cultivation fields between May and July, 2009. Two Bacillus subtilis strains were applied to nature-friendly cultivation fields as biocontrol agents during the sampling period. Relative abundances of bacteria and plant pathogenic fungi related T-RFs were also measured to monitor the effect of biocontrol agents on potential plant pathogenic fungi. In the principal component analysis (PCA) based on T-RFLP profiles, the microbial communities from rhizosphere soil samples in July, including bacteria and fungi, showed distinct difference between nature-friendly cultivation fields and other cultivation fields. However, there was no correlation between cultivation methods and leaf microbial communities at any sampling period. Changes in the abundance of bacteria related T-RF in the rhizosphere of nature-friendly cultivation fields were observed clearly two months after application of biocontrol agent, while the abundance of plant pathogenic fungi related T-RFs significantly decreased.     

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors

Vector-borne microbes are subject to the ecological constraints of two distinct microenvironments: that in the arthropod vector and that in the blood of its vertebrate host. Because the structure of bacterial communities in these two microenvironments may substantially affect the abundance of vector-borne microbes, it is important to understand the relationship between bacterial communities in both microenvironments and the determinants that shape them. We used pyrosequencing analyses to compare the structure of bacterial communities in Synosternus cleopatrae fleas and in the blood of their Gerbillus andersoni hosts. We also monitored the interindividual and seasonal variability in these bacterial communities by sampling the same individual wild rodents during the spring and again during the summer. We show that the bacterial communities in each sample type (blood, female flea or male flea) had a similar phylotype composition among host individuals, but exhibited seasonal variability that was not directly associated with host characteristics. The structure of bacterial communities in male fleas and in the blood of their rodent hosts was remarkably similar and was dominated by flea-borne Bartonella and Mycoplasma phylotypes. A lower abundance of flea-borne bacteria and the presence of Wolbachia phylotypes distinguished bacterial communities in female fleas from those in male fleas and in rodent blood. These results suggest that the overall abundance of a certain vector-borne microbe is more likely to be determined by the abundance of endosymbiotic bacteria in the vector, abundance of other vector-borne microbes co-occurring in the vector and in the host blood and by seasonal changes, than by host characteristics.     

Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans.     

Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater,Marine, and Hypersaline Water-Containing Microcosms

Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.     

Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco (Nicotiana tabacum L.)

Microorganisms of plant phyllosphere play an important role in plant health and productivity and are influenced by abiotic and biotic factors. In this study, we investigated the phyllosphere bacterial communities of three cigar tobacco varieties cultivated in Guangcun (GC) and Wuzhishan (WZS), Hainan, China. Metagenomic DNA was extracted from tobacco leaf samples and sequenced by 16S rDNA amplicon sequencing. Our results showed that bacterial communities of cigar tobacco phyllosphere in GC exhibited remarkably higher alpha diversity than that in WZS. There was slight effect of tobacco genotype variations on the alpha diversity in both cultivation sites, and beta diversity and structure of bacterial community were not influenced significantly by the cultivation sites and tobacco varieties. Statistical analyses of species diversity unraveled that the dominant species in bacterial communities of cigar tobacco phyllosphere among all these samples were phylogenetically affiliated to Proteobacteria and Cyanobacteria. At the genus level, the most abundant microorganism was Limnobacter, followed by Brevundimonas, unidentified_Cyanobacteria, and Pseudomonas. Additionally, environmental conditions except for humidity were negatively correlated with the relative abundance of bacterial genera. Further analyses revealed that influence of site‐specific factors on tobacco bacterial community was relatively higher than genotype‐specific factors. In short, this study may contribute to the knowledge base of practical applications of bacterial inoculants for tobacco leaf production.     

Nonnative plant shifts functional groups of arthropods following drought

Nonnative plants alter the composition of native plant communities, with concomitant effects on arthropods. However, plant invasions may not be the only disturbance affecting native communities, and multiple disturbances can have compounding effects. We assessed the effects of invasion and drought on plant and arthropod communities by comparing grasslands dominated by nonnative Old World bluestem grasses (OWBs, Dichanthium annulatum) to grasslands dominated by native plants during a period of decreasing drought severity (2011–2013). Native plant communities had more species of plants and arthropods (/m²) than areas dominated by OWBs during extreme drought, but richness was comparable as drought severity decreased. Abundance of arthropods was greater in native plant communities than in OWB communities during extreme drought, but OWB communities had more arthropods during moderate and non-drought conditions. We observed a shift in the arthropod community from one dominated by detritivores to one dominated by herbivores following plant invasion; the magnitude of this shift increased as drought severity decreased. Both plant communities were dominated by nonnative arthropods. A nonnative leafhopper (Balclutha rubrostriata) and native mites (Mochlozetidae) dominated OWB communities as drought severity decreased, and OWBs may serve as refugia for both taxa. Nonnative woodlice (Armadillidium vulgare) dominated native plant communities during extreme and non-drought conditions and abundance of this species may be associated with an increase in plant litter and available nutrients. Given the importance of arthropods for ecosystem services, incorporating arthropod data into conservation studies may demonstrate how changes in arthropod diversity alter ecosystem function where nonnative plants are dominant.     

Host-specificity of moss-associated fungal communities in the Ny-Ålesund region (Svalbard,High Arctic) as revealed by amplicon pyrosequencing

Fungal communities play a significant role in regulating ecological processes in the Arctic tundra. However, the extent to which the Arctic moss species and host types (moss, lichen and vascular plant) determine the richness, diversity, and composition of fungal communities at a local scale has not been quantitatively explored. Using 454 pyrosequencing in the current study, we characterized the fungal communities associated with six moss species (Andreaea rupestris, Bryum pseudotriquetrum, Hymenoloma crispulum, Polytrichastrum alpinum, Racomitrium lanuginosum, and Sanionia uncinata) and compared them with fungal communities associated with lichens and vascular plants in the Ny-Ålesund region (High Arctic). Host-species preference had greater explanatory power than geographical factors (longitude, latitude, elevation) in shaping moss-associated fungal communities. Fungal communities associated with mosses differed significantly from those associated with vascular plants and lichens, suggesting specificity of the fungal communities among three host types. Pairwise comparison analysis also indicated that the relative abundance of many taxonomic groups (e.g., Chaetothyriales, Leotiales, Catenulifera, Alatospora, and Toxicocladosporium) significantly differed between mosses and the other two host types. These results suggest host factors significantly affect the distribution of the fungal species associated with these moss species in the local-scale Arctic tundra.     

Progressive and retrogressive ecosystem development coincide with soil bacterial community change in a dune system under lowland temperate rainforest in New Zealand

Background

It is established that plant communities show patterns of change linked to progressive and retrogressive stages of ecosystem development. It is not known, however, whether bacterial communities also show similar patterns of change associated with long-term ecosystem development.

Methods

We studied soil bacterial communities along a 6,500 year dune chronosequence under lowland temperate rain forest at Haast, New Zealand. Pyrosequencing of 16S rRNA genes was used to observe structural change in bacterial communities during the process of pedogenesis and ecosystem development.

Results

Bacterial communities showed patterns of change during pedogenesis, with the largest change during the first several hundred years after dune stabilization. The most abundant bacterial taxa were Alphaproteobacteria, Actinobacteria and Acidobacteria. These include taxa most closely related to nitrogen-fixing bacteria, and suggest heterotrophic nitrogen input may be important throughout the chronosequence. Changes in bacterial community structure were related to changes in several soil properties, including total phosphorus, C:N ratio, and pH. The Bacteroidetes, Actinobacteria, Cyanobacteria, Firmicutes, and Betaproteobacteria all showed a general decline in abundance as pedogenesis proceeded, while Acidobacteria, Alphaproteobacteria, and Plantctomycetes tended to increase as soils aged.

Conclusions

There were trends in the dynamics of bacterial community composition and structure in soil during ecosystem development. Bacterial communities changed in ways that appear to be consistent with a model of ecosystem progression and retrogression, perhaps indicating fundamental processes underpin patterns of below and above-ground community change during ecosystem development.     

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata

Biotic interactions dominate plankton communities, yet the microbial consortia associated with harmful algal blooms (HABs) have not been well-described. Here, high-throughput amplicon sequencing of ribosomal genes was used to quantify the dynamics of bacterial (16S) and phytoplankton assemblages (18S) associated with blooms and cultures of two harmful algae, Alexandrium fundyense and Dinophysis acuminata. Experiments were performed to assess changes in natural bacterial and phytoplankton communities in response to the filtrate from cultures of these two harmful algae. Analysis of prokaryotic sequences from ecosystems, experiments, and cultures revealed statistically unique bacterial associations with each HAB. The dinoflagellate, Alexandrium, was strongly associated with multiple genera of Flavobacteria including Owenweeksia spp., Maribacter spp., and individuals within the NS5 marine group. While Flavobacteria also dominated Dinophysis-associated communities, the relative abundance of Alteromonadales bacteria strongly co-varied with Dinophysis abundances during blooms and Ulvibacter spp. (Flavobacteriales) and Arenicella spp. (Gammaproteobacteria) were associated with cells in culture. Eukaryotic sequencing facilitated the discovery of the endosymbiotic, parasitic dinoflagellate, Amoebophrya spp., that had not been regionally described but represented up to 17% of sequences during Alexandrium blooms. The presence of Alexandrium in field samples and in experiments significantly altered the relative abundances of bacterial and phytoplankton by both suppressing and promoting different taxa, while this effect was weaker in Dinophysis. Experiments specifically revealed a negative feedback loop during blooms whereby Alexandrium filtrate promoted the abundance of the parasite, Amoebophrya spp. Collectively, this study demonstrates that HABs formed by Alexandrium and Dinophysis harbor unique prokaryotic and eukaryotic microbiomes that are likely to, in turn, influence the dynamics of these HABs.     

Experimental study of Microcystis-associated and free-living bacteria

In the experiment with water from the hypereutrophic Lake Frederiksborg Slotso (Denmark) sampled during the autumn peak of Microcystis growth, the quantity and production of free-living and cyanobacteria-associated heterotrophic bacteria were determined, as well as the extracellular enzymatic (aminopeptidase) activity. The functional diversities of associated and free-living bacterial communities were additionally compared using BIOLOG GN microplates to reveal the possible export of Microcystis-attached bacteria into ambient water. It has been shown that the cell size, production values, and growth rates of associated bacteria were less than those of free-living bacteria. At the same time, the potential aminopeptidase activity of associated bacteria was always higher than that of free-living bacteria. The experimental results have shown significant compositional differences in the structure of bacterial communities from different habitats.     

Chinese white truffles shape the ectomycorrhizal microbial communities of Corylus avellana

Here, we investigated the influence of Chinese white truffle (Tuber panzhihuanense) symbioses on the microbial communities associated with Corylus avellana during the early development stage of symbiosis. The microbial communities associated with ectomycorrhizae, and associated with roots without T. panzhihuanense colonization, were determined via high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS genes. Microbial community diversity was higher in the communities associated with the ectomycorrhizae than in the control treatment. Further, bacterial and fungal community structures were different in samples containing T. panzhihuanense in association with C. avellana compared to the control samples. In particular, the bacterial genera Rhizobium, Pedomicrobium, and Herbiconiux were more abundant in the ectomycorrhizae, in addition to the fungal genus Monographella. Moreover, there were clear differences in some physicochemical properties among the rhizosphere soils of the two treatments. Statistical analyses indicated that soil properties including exchangeable magnesium and exchangeable calcium prominently influenced microbial community structure. Lastly, inference of bacterial metabolic functions indicated that sugar and protein metabolism functions were significantly more enriched in the communities associated with the ectomycorrhizae from C. avellana mycorrhized with T. panzhihuanense compared to communities from roots of cultivated C. avellana without T. panzhihuanense. Taken together, these results highlight the interactions among ectomycorrhizal fungi, soil properties, and microbial communities that are associated with host plants and further our understanding of the ecology and cultivation of the economically important T. panzhihuanense truffles.