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1.  Phenotypic and physiological characterization of the epibiotic interaction between TM7x and its basibiont Actinomyces 
Microbial ecology  2015;71(1):243-255.
Despite many examples of obligate epibiotic symbiosis (one organism living on the surface of another) in nature, such an interaction has rarely been observed between two bacteria. Here, we further characterize a newly reported interaction between a human oral obligate parasitic bacterium TM7x (cultivated member of Candidatus Saccharimonas formerly Candidate Phylum TM7), and its basibiont Actinomyces odontolyticus species (XH001), providing a model system to study epiparasitic symbiosis in the domain Bacteria. Detailed microscopic studies indicate that both partners display extensive morphological changes during symbiotic growth. XH001 cells manifested as short rods in monoculture, but displayed elongated and hyphal morphology when physically associated with TM7x. Interestingly, these dramatic morphological changes in XH001 were also induced in oxygen-depleted conditions, even in the absence of TM7x. Targeted qRT-PCR analyses revealed that both the physical association with TM7x as well as oxygen depletion triggered up-regulation of key stress response genes in XH001, and in combination, these conditions act in an additive manner. TM7x and XH001 co-exist with relatively uniform cell morphologies under nutrient-replete conditions. However, upon nutrient depletion, TM7x-associated XH001 displayed a variety of cell morphologies, including swollen cell body, clubbed ends and even cell lysis, and a large portion of TM7x cells transformed from ultrasmall cocci into elongated cells. Our study demonstrates a highly dynamic interaction between epibiont TM7x and its basibiont XH001 in response to physical association or environmental cues such as oxygen level and nutritional status, as reflected by their morphological and physiological changes during symbiotic growth.
PMCID: PMC4688200  PMID: 26597961
Obligate; epibiont; symbiosis; bacterial interaction; TM7; Actinomyces
2.  Minimally invasive sampling method identifies differences in taxonomic richness of nasal microbiomes in young infants associated with mode of delivery 
Microbial ecology  2015;71(1):233-242.
To date, there is a limited understanding of the role of the airway microbiome in the early-life development of respiratory diseases such as asthma, partly due to a lack of simple and minimally invasive sample collection methods. In order to characterize the baseline microbiome of the upper respiratory tract (URT) in infants, a comparatively non-invasive method for sampling the URT microbiome suitable for use in infants was developed. Microbiome samples were collected by placing filter paper in the nostrils of thirty-three healthy, term infants enrolled as part of the Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure (INSPIRE) study. After bacterial genomic DNA was extracted from the filters, amplicons were generated with universal primers targeting the V1 – V3 region of the 16S rRNA gene. This method was capable of capturing a wide variety of taxa expected to inhabit the nasal cavity. Analyses stratifying subjects by demographic and environmental factors previously observed or predicted to influence microbial communities were performed. Microbial community richness was found to be higher in infants who had been delivered via Cesarean section and in those who had been formula-fed; an association was observed between diet and delivery, which confounds this analysis. We have established a baseline URT microbiome using a non-invasive filter paper nasal sampling for this population and future studies will be performed in this large observational cohort of infants to investigate the relationship between viral infections, the URT microbiota, and the development of childhood wheezing illnesses.
PMCID: PMC4688197  PMID: 26370110
microbiome; 16S rRNA; next-generation sequencing; upper respiratory tract
3.  Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation 
Microbial ecology  2016;72(2):470-478.
Gut microbes are essential for the degradation of dietary oxalate, and this function may play a role in decreasing the incidence of kidney stones. However, many oxalate-degrading bacteria are susceptible to antibiotics and the use of oxalate-degrading probiotics has only led to an ephemeral reduction in urinary oxalate. The objective of the current study was to determine the efficacy of using whole-community microbial transplants from a wild mammalian herbivore, Neotoma albigula, to increase oxalate degradation over the long term in the laboratory rat, Rattus norvegicus. We quantified the change in total oxalate degradation in lab rats immediately after microbial transplants and at 2- and 9-month intervals following microbial transplants. Additionally, we tracked the fecal microbiota of the lab rats, with and without microbial transplants, using high-throughput Illumina sequencing of a hyper-variable region of the 16S rRNA gene. Microbial transplants resulted in a significant increase in oxalate degradation, an effect that persisted 9 months after the initial transplants. Functional persistence was corroborated by the transfer, and persistence of a group of bacteria previously correlated with oxalate consumption in N. albigula, including an anaerobic bacterium from the genus Oxalobacter known for its ability to use oxalate as a sole carbon source. The results of this study indicate that whole-community microbial transplants are an effective means for the persistent colonization of oxalate-degrading bacteria in the mammalian gut.
PMCID: PMC5155304  PMID: 27312892
Gut microbiota; Dietary oxalate; Microbial transplant; Urinary oxalate
4.  Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions 
Microbial Ecology  2016;73(1):236-252.
In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1—day 3; T2—day 5), contact between both partner organisms was absent, whereas in the final stage (T3—day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime. In the system, B. terrae BS001 apparently perceived the presence of the fungal hyphae already at the early experimental stages (T1, T2), by strongly upregulating a suite of chemotaxis and flagellar motility genes. With respect to specific metabolism and energy generation, a picture of differential involvement in different metabolic routes was obtained. Initial (T1, T2) up- or downregulation of ethanolamine and mandelate uptake and utilization pathways was substituted by a strong investment, in the presence of the fungus, in the expression of putative metabolic gene clusters (T3). Specifically at T3, five clustered genes that are potentially involved in energy generation coupled to an oxidative stress response, and two genes encoding short-chain dehydrogenases/oxidoreductases (SDR), were highly upregulated. In contrast, the dnaE2 gene (related to general stress response; encoding error-prone DNA polymerase) was transcriptionally downregulated at this stage. This study revealed that B. terrae BS001, from a stress-induced state, resulting from the soil extract agar milieu, responds positively to fungal hyphae that encroach upon it, in a temporally dynamic manner. The response is characterized by phases in which the modulation of (1) chemotaxis, (2) metabolic activity, and (3) oxidative stress responses are key mechanisms.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0885-7) contains supplementary material, which is available to authorized users.
PMCID: PMC5209427  PMID: 27844108
Chemotaxis; Short-chain dehydrogenases; Oxidative stress; Metabolic potential; Bacterial-fungal interactions
5.  A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil 
Microbial Ecology  2016;73(1):61-74.
With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four flood-pulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011–2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes. We report here a global comparison of the bacterioplankton makeup of freshwater systems, focusing on a comparison of Brazilian lakes with similar freshwater systems across the globe. The results indicate a surprising similarity at higher taxonomic levels of the bacterioplankton in Brazilian freshwater with global sites. However, substantial novel diversity at the family level was also observed for the Brazilian freshwater systems. Brazilian freshwater bacterioplankton richness was relatively average globally. Ordination results indicate that Brazilian bacterioplankton composition is unique from other areas of the globe. Using Brazil-only ordinations, floodplain system differentiation most strongly correlated with dissolved oxygen, pH, and phosphate. Our data on Brazilian freshwater systems in combination with analysis of a collection of freshwater environmental samples from across the globe offers the first regional picture of bacterioplankton diversity in these important freshwater systems.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0834-5) contains supplementary material, which is available to authorized users.
PMCID: PMC5209421  PMID: 27613296
Bacterioplankton; Diversity; Floodplain lakes; Brazil; Metagenomics; Paraná; Pantanal Amazon; Araguaia
6.  Abundance of Class 1 Integron-Integrase and Sulfonamide Resistance Genes in River Water and Sediment Is Affected by Anthropogenic Pressure and Environmental Factors 
Microbial Ecology  2016;72(4):909-916.
In this study, we determined the presence of class 1 integron-integrase gene in culturable heterotrophic bacteria isolated from river water and sediment sampled upstream and downstream of a wastewater treatment plant effluent discharge. Moreover, we quantified intI1 and sulfonamide resistance genes (sul1 and sul2) in the water and sediment using qPCR. There was no correlation between the results from water and sediment samples, which suggests integron-containing bacteria are differentially retained in these two environmental compartments. The discharge of treated wastewater significantly increased the frequency of intI1 among culturable bacteria and the gene copy number in river water, and increased the number of sul1 genes in the sediment. We also observed seasonal differences in the frequency of the class 1 integron-integrase gene among culturable heterotrophs as well as intI1 copy number in water, but not in sediment. The results suggest that the abundance of class 1 integrons in aquatic habitat depends on anthropogenic pressure and environmental factors.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0843-4) contains supplementary material, which is available to authorized users.
PMCID: PMC5080314  PMID: 27599709
Integron; Wastewater; Surface water; Seasonality
7.  Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes 
Microbial Ecology  2016;73(1):162-176.
The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0837-2) contains supplementary material, which is available to authorized users.
PMCID: PMC5209426  PMID: 27581036
Soil metagenomes; Next-generation sequencing; Nitrogen-fixing bacteria; Arable soils; Wastelands
8.  What Underpins the Trophic Networks of the Plankton in Shallow Oxbow Lakes? 
Microbial Ecology  2016;73(1):17-28.
The aim of this study was to determine the relationships in the microbial trophic network underpinning them about communities of plankton ciliates in shallow oxbow lakes of the Vistula River in southern Poland (Jeziorzany 1, Jeziorzany 2, Piekary, Tyniec). The plankton components (phytoplankton, ciliates, zooplankton) were grouped by dietary preference. The studied oxbows differed in physicochemical parameters and in phytoplankton. Cyanobacteria dominated in the total biomass of phytoplankton in the Tyniec oxbow, big green algae (>30 μm) in Piekary and Jeziorzany 1, and euglenoids in Jeziorzany 2 oxbow. The dominance pattern of ciliates and zooplankton were similar in all oxbows. Algivorous ciliates were the main dominant ciliates, and among zooplankton the dominant ones were herbivores that feed on small algae (<30 μm). The oxbows differed significantly in total phytoplankton biomass, cyanobacteria biomass, euglenoid biomass, small green algae (<30 μm) biomass, total biomass of zooplankton, biomass of zooplankton feeding on bacteria + algae, and biomass of zooplankton feeding on big algae (>30 μm). There was no significant differences in ciliate biomass between oxbows. In redundancy analyses, the variability at the trophic groups of plankton was described by explanatory variables in 42.3 %, and positive relationships were found: e.g., between omnivorous zooplankton biomass, the biomass of ciliates feeding on bacteria + algae, and NH4 level; between euglenoid biomass and dinoflagellate biomass; and between cyanobacteria biomass and bacterivorous ciliate biomass. Spearman correlation analysis revealed several relationships between different groups of plankton. In general, phytoplankton group shows more connection among themselves and with different zooplankton groups, e.g., phytoplankton biomass with herbivorous zooplankton biomass (−0.33); and cyanobacteria biomass with dinoflagellate biomass (0.65). Ciliates showed more connections among their trophic groups (e.g., algivorous ciliate biomass with omnivorous ciliate biomass, 0.78) and with zooplankton trophic groups (e.g., biomass of algivorous + bacterivorous ciliates with biomass of predator zooplankton, −0.36). Simple correlations analysis revealed the trophic food web network connectivity among plankton organisms, indicating the flow of organic matter from phytoplankton to zooplankton and from ciliates to zooplankton. Our study sheds light on the trophic relations among plankton ciliates, which are neglected in research but often form a large percentage of zooplankton biomass. In the studied oxbows, ciliate forms 6.7 % of total zooplankton biomass in Jeziorzany 1 and up to 44.5 % of it in the Piekary oxbow.
PMCID: PMC5209435  PMID: 27544677
Trophic networks; Ciliates; Zooplankton; Phytoplankton; Oxbow lakes
9.  Listeria monocytogenes Inhibits Serotonin Transporter in Human Intestinal Caco-2 Cells 
Microbial Ecology  2016;72(3):730-739.
Listeria monocytogenes is a Gram-positive bacterium that can cause a serious infection. Intestinal microorganisms have been demonstrated to contribute to intestinal physiology not only through immunological responses but also by modulating the intestinal serotonergic system. Serotonin (5-HT) is a neuromodulator that is synthesized in the intestinal epithelium and regulates the whole intestinal physiology. The serotonin transporter (SERT), located in enterocytes, controls intestinal 5-HT availability and therefore serotonin’s effects. Infections caused by L. monocytogenes are well described as being due to the invasion of intestinal epithelial cells; however, the effect of L. monocytogenes on the intestinal epithelium remains unknown. The main aim of this work, therefore, was to study the effect of L. monocytogenes on SERT. Caco2/TC7 cell line was used as an enterocyte-like in vitro model, and SERT functional and molecular expression assays were performed. Our results demonstrate that living L. monocytogenes inhibits serotonin uptake by reducing SERT expression at the brush border membrane. However, neither inactivated L. monocytogenes nor soluble metabolites were able to affect SERT. The results also demonstrate that L. monocytogenes yields TLR2 and TLR10 transcriptional changes in intestinal epithelial cells and suggest that TLR10 is potentially involved in the inhibitory effect observed on SERT. Therefore, L. monocytogenes, through TLR10-mediated SERT inhibition, may induce increased intestinal serotonin availability and potentially contributing to intestinal physiological changes and the initiation of the inflammatory response.
PMCID: PMC5023727  PMID: 27488594
5-HT; SERT; Intestinal epithelium; Listeriosis; TLR
10.  High Life Expectancy of Bacteria on Lichens 
Microbial Ecology  2016;72(3):510-513.
Self-sustaining lichen symbioses potentially can become very old, sometimes even thousands of years in nature. In the joint structures, algal partners are sheltered between fungal structures that are externally colonized by bacterial communities. With this arrangement lichens survive long periods of drought, and lichen thalli can be revitalized even after decades of dry storage in a herbarium. To study the effects of long-term ex situ storage on viability of indigenous bacterial communities we comparatively studied herbarium-stored material of the lung lichen, Lobaria pulmonaria. We discovered that a significant fraction of the lichen-associated bacterial community survives herbarium storage of nearly 80 years, and living bacteria can still be found in even older material. As the bacteria reside in the upper surface layers of the lichen material, we argue that the extracellular polysaccharides of lichens contribute to superior life expectancy of bacteria. Deeper understanding of underlying mechanisms could provide novel possibilities for biotechnological applications.
PMCID: PMC5023722  PMID: 27464604
Herbarium; Storage; Thallus; Survival; Lichen-associated bacteria; Lobaria pulmonaria
11.  Fungal endophytes in above-ground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts 
Microbial ecology  2015;70(1):61-76.
In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in above-ground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on non-succulent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region, and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less-arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert plant communities, and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.
PMCID: PMC4457668  PMID: 25645243
Arid lands; Ascomycota; diversity; Dothideomycetes; fungi; Larrea; phylogeny; Parkinsonia; Preussia; Simmondsia; symbiosis
12.  The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants 
Microbial Ecology  2016;72:394-406.
Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0779-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4937074  PMID: 27245598
Vascular plants; Upward migration; Subnival soil; Plant-associated bacteria
13.  Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms 
Microbial Ecology  2016;72:479-492.
Nitrate is emerging as a possible health benefactor. Especially the microbial conversion of nitrate to nitrite in the oral cavity and the subsequent conversion to nitric oxide in the stomach are of interest in this regard. Yet, how nitrate influences the composition and biochemistry of the oral ecosystem is not fully understood. To investigate the effect of nitrate on oral ecology, we performed a 4-week experiment using the multiplaque artificial mouth (MAM) biofilm model. This model was inoculated with stimulated saliva of two healthy donors. Half of the microcosms (n = 4) received a constant supply of nitrate, while the other half functioned as control (n = 4). Additionally, all microcosms received a nitrate and sucrose pulse, each week, on separate days to measure nitrate reduction and acid formation. The bacterial composition of the microcosms was determined by 16S rDNA sequencing. The origin of the saliva (i.e., donor) showed to be the strongest determinant for the development of the microcosms. The supplementation of nitrate was related to a relatively high abundance of Neisseria in the microcosms of both donors, while Veillonella was highly abundant in the nitrate-supplemented microcosms of only one of the donors. The lactate concentration after sucrose addition was similarly high in all microcosms, irrespective of treatment or donor, while the concentration of butyrate was lower after nitrate addition in the nitrate-receiving microcosms. In conclusion, nitrate influences the composition and biochemistry of oral microcosms, although the result is strongly dependent on the inoculum.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0775-z) contains supplementary material, which is available to authorized users.
PMCID: PMC4937104  PMID: 27155967
Oral microbiome; Nitrate reduction; Short chain fatty acids; Veillonella; Neisseria
14.  Bats Increase the Number of Cultivable Airborne Fungi in the “Nietoperek” Bat Reserve in Western Poland 
Microbial Ecology  2016;72:36-48.
The “Nietoperek” bat reserve located in Western Poland is one of the largest bat hibernation sites in the European Union with nearly 38,000 bats from 12 species. Nietoperek is part of a built underground fortification system from WWII. The aims of the study were (1) to determine the fungal species composition and changes during hibernation season in relation to bat number and microclimatic conditions and (2) evaluate the potential threat of fungi for bat assemblages and humans visiting the complex. Airborne fungi were collected in the beginning, middle and end of hibernation period (9 November 2013 and 17 January and 15 March 2014) in 12 study sites, one outside and 11 inside the complex. Ambient temperature (Ta) and relative humidity (RH) were measured by the use of data loggers, and species composition of bats was recorded from the study sites. The collision method (Air Ideal 3P) sampler was used to detect 34 species of airborne fungi including Pseudogymnoascus destructans (Pd). The density of airborne fungi isolated from the outdoor air samples varied from 102 to 242 CFU/1 m3 of air and from 12 to 1198 CFU in the underground air samples. There was a positive relationship between number of bats and the concentration of fungi. The concentration of airborne fungi increased with the increase of bats number. Analysis of other possible ways of spore transport to the underground indicated that the number of bats was the primary factor determining the number of fungal spores in that hibernation site. Microclimatic conditions where Pd was found (median 8.7 °C, min-max 6.1–9.9 °C and 100 %, min-max 77.5–100.0 %) were preferred by hibernating Myotis myotis and Myotis daubentonii; therefore, these species are most probably especially prone to infection by this fungi species. The spores of fungi found in the underground can be pathogenic for humans and animals, especially for immunocompromised persons, even though their concentrations did not exceed limits and norms established as dangerous for human health. In addition, we showed for the first time that the air in bats hibernation sites can be a reservoir of Pd. Therefore, further study in other underground environments and wintering bats is necessary to find out more about the potential threat of airborne fungi to bats and public health.
PMCID: PMC4902831  PMID: 27084554
Airborne fungi; Bats; “Nietoperek” bat reserve; Pseudogymnoascus destructans
15.  Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors? 
Microbial Ecology  2016;72:207-220.
Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0748-2) contains supplementary material, which is available to authorized users.
PMCID: PMC4902835  PMID: 26961712
Soil metagenomics; Climate change; Elevational gradient; Bacteria; Archaea; Fungi
16.  Toxicity Overrides Morphology on Cylindrospermopsis raciborskii Grazing Resistance to the Calanoid Copepod Eudiaptomus gracilis 
Microbial Ecology  2016;71:835-844.
Toxicity and morphology may function as defense mechanisms of bloom-forming cyanobacteria against zooplankton grazing. Yet, the relative importance of each of these factors and their plasticity remains poorly known. We tested the effects of chemical and morphological traits of the bloom-forming cyanobacterium Cylindrospermopsis raciborskii on the feeding response of the selective feeder Eudiaptomus gracilis (Calanoida, Copepoda), using a saxitoxin-producing strain (STX+) and a non-saxitoxin (STX−)-producing strain as food. From these two chemotypes, we established cultures of three different morphotypes that differed in filament length (short, medium, and long) by incubating the strains at 17, 25, and 32 °C. We hypothesized that the inhibitory effects of saxitoxins determine the avoidance of C. raciborskii, and that morphology would only become relevant in the absence of saxitoxins. Temperature affected two traits: higher temperature resulted in significantly shorter filaments in both strains and led to much higher toxin contents in the STX+ strain (1.7 μg eq STX L−1 at 17 °C, 7.9 μg eq STX L−1 at 25 °C, and 25.1 μg eq STX L−1 at 32 °C). Copepods strongly reduced the ingestion of the STX+ strain in comparison with STX− cultures, regardless of filament length. Conversely, consumption of shorter filaments was significantly higher in the STX− strain. The great plasticity of morphological and chemical traits of C. raciborskii and their resultant contrasting effects on the feeding behavior of zooplankton might explain the success of this cyanobacterium in a variety of aquatic environments.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0734-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4823325  PMID: 26888523
Cyanobacteria; Feeding inhibition; Harmful algal blooms; Saxitoxins; Temperature; Zooplankton
17.  Inter-Population Variability of Endosymbiont Densities in the Asian Citrus Psyllid (Diaphorina citri Kuwayama) 
Microbial Ecology  2016;71:999-1007.
The Asian citrus psyllid (Diaphorina citri Kuwayama) is an insect pest capable of transmitting Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening in North America. D. citri also harbors three endosymbionts, Wolbachia, Candidatus Carsonella ruddii, and Candidatus Profftella armatura, which may influence D. citri physiology and fitness. Although genomic researches on these bacteria have been conducted, much remains unclear regarding their ecology and inter-population variability in D. citri. The present work examined the densities of each endosymbiont in adult D. citri sampled from different populations using quantitative PCR. Under field conditions, the densities of all three endosymbionts positively correlated with each other, and they are associated with D. citri gender and locality. In addition, the infection density of CLas also varied across populations. Although an analysis pooling D. citri from different populations showed that CLas-infected individuals tended to have lower endosymbiont densities compared to uninfected individuals, the difference was not significant when the population was included as a factor in the analysis, suggesting that other population-specific factors may have stronger effects on endosymbiont densities. To determine whether there is a genetic basis to the density differences, endosymbiont densities between aged CLas-negative females of two D. citri populations reared under standardized laboratory conditions were compared. Results suggested that inter-population variability in Wolbachia infection density is associated with the genotypes of the endosymbiont or the host. Findings from this work could facilitate understanding of D. citri-bacterial associations that may benefit the development of approaches for managing citrus greening, such as prevention of CLas transmission.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-016-0733-9) contains supplementary material, which is available to authorized users.
PMCID: PMC4944574  PMID: 26846216
Huanglongbing; Intracellular endosymbionts; Primary endosymbionts; Bacteriome
18.  Significance and Roles of Proteus spp. Bacteria in Natural Environments 
Microbial Ecology  2016;72(4):741-758.
Proteus spp. bacteria were first described in 1885 by Gustav Hauser, who had revealed their feature of intensive swarming growth. Currently, the genus is divided into Proteus mirabilis, Proteus vulgaris, Proteus penneri, Proteus hauseri, and three unnamed genomospecies 4, 5, and 6 and consists of 80 O-antigenic serogroups. The bacteria are known to be human opportunistic pathogens, isolated from urine, wounds, and other clinical sources. It is postulated that intestines are a reservoir of these proteolytic organisms. Many wild and domestic animals may be hosts of Proteus spp. bacteria, which are commonly known to play a role of parasites or commensals. However, interesting examples of their symbiotic relationships with higher organisms have also been described. Proteus spp. bacteria present in soil or water habitats are often regarded as indicators of fecal pollution, posing a threat of poisoning when the contaminated water or seafood is consumed. The health risk may also be connected with drug-resistant strains sourcing from intestines. Positive aspects of the bacteria presence in water and soil are connected with exceptional features displayed by autochthonic Proteus spp. strains detected in these environments. These rods acquire various metabolic abilities allowing their adaptation to different environmental conditions, such as high concentrations of heavy metals or toxic substances, which may be exploited as sources of energy and nutrition by the bacteria. The Proteus spp. abilities to tolerate or utilize polluting compounds as well as promote plant growth provide a possibility of employing these microorganisms in bioremediation and environmental protection.
PMCID: PMC5080321  PMID: 26748500
Natural microflora; Symbionts; Pathogens; Fecal pollution; Bioremediation; PGPR
19.  Wildly Growing Asparagus (Asparagus officinalis L.) Hosts Pathogenic Fusarium Species and Accumulates Their Mycotoxins 
Microbial Ecology  2015;71:927-937.
Asparagus officinalis L. is an important crop in many European countries, likely infected by a number of Fusarium species. Most of them produce mycotoxins in plant tissues, thus affecting the physiology of the host plant. However, there is lack of information on Fusarium communities in wild asparagus, where they would definitely have considerable environmental significance. Therefore, the main scientific aim of this study was to identify the Fusarium species and quantify their typical mycotoxins present in wild asparagus plants collected at four time points of the season. Forty-four Fusarium strains of eight species—Fusarium acuminatum, Fusarium avenaceum, Fusarium culmorum, Fusarium equiseti, Fusarium oxysporum, Fusarium proliferatum, Fusarium sporotrichioides, and Fusarium tricinctum—were isolated from nine wild asparagus plants in 2013 season. It is the first report of F. sporotrichioides isolated from this particular host. Fumonisin B1 was the most abundant mycotoxin, and the highest concentrations of fumonisins B1–B3 and beauvericin were found in the spears collected in May. Moniliformin and enniatins were quantified at lower concentrations. Mycotoxins synthesized by individual strains obtained from infected asparagus tissues were assessed using in vitro cultures on sterile rice grain. Most of the F. sporotrichioides strains synthesized HT-2 toxin and F. equiseti strains were found to be effective zearalenone producers.
PMCID: PMC4823322  PMID: 26687343
Fumonisins; Fungal plant pathogens; Molecular identification; Natural Fusarium populations; Trichothecenes; Zearalenone
20.  Allochthonous Carbon—a Major Driver of Bacterioplankton Production in the Subarctic Northern Baltic Sea 
Microbial Ecology  2015;71:789-801.
Heterotrophic bacteria are, in many aquatic systems, reliant on autochthonous organic carbon as their energy source. One exception is low-productive humic lakes, where allochthonous dissolved organic matter (ADOM) is the major driver. We hypothesized that bacterial production (BP) is similarly regulated in subarctic estuaries that receive large amounts of riverine material. BP and potential explanatory factors were measured during May–August 2011 in the subarctic Råne Estuary, northern Sweden. The highest BP was observed in spring, concomitant with the spring river-flush and the lowest rates occurred during summer when primary production (PP) peaked. PLS correlations showed that ∼60 % of the BP variation was explained by different ADOM components, measured as humic substances, dissolved organic carbon (DOC) and coloured dissolved organic matter (CDOM). On average, BP was threefold higher than PP. The bioavailability of allochthonous dissolved organic carbon (ADOC) exhibited large spatial and temporal variation; however, the average value was low, ∼2 %. Bioassay analysis showed that BP in the near-shore area was potentially carbon limited early in the season, while BP at seaward stations was more commonly limited by nitrogen-phosphorus. Nevertheless, the bioassay indicated that ADOC could contribute significantly to the in situ BP, ∼60 %. We conclude that ADOM is a regulator of BP in the studied estuary. Thus, projected climate-induced increases in river discharge suggest that BP will increase in subarctic coastal areas during the coming century.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-015-0714-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4823372  PMID: 26677860
Allochthonous organic matter; Carbon utilization; Bacterioplankton production; Sub-arctic estuary; Baltic Sea
21.  Fungal Community Assembly in the Amazonian Dark Earth 
Microbial Ecology  2015;71:962-973.
Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in ADE soils were more similar to each other than their ADJ soils, except for only one site. Phosphorus and aluminum saturation were the main soil chemical factors contributing to ADE and ADJ fungal community dissimilarities. Differences in fungal richness were not observed between ADE and ADJ soil pairs regarding to the most sites. In general, the most dominant subphyla present in the soils were Pezizomycotina, Agaricomycotina, and Mortierellomycotina. The most abundant operational taxonomic units (OTUs) in ADE showed similarities with the entomopathogenic fungus Cordyceps confragosa and the saprobes Fomitopsis pinicola, Acremonium vitellinum, and Mortierellaceae sp., whereas OTUs similar to Aspergillus niger, Lithothelium septemseptatum, Heliocephala gracillis, and Pestalosphaeria sp. were more abundant in ADJ soils. Differences in fungal community composition were associated to soil chemical factors in ADE (P, Ca, Zn, Mg, organic matter, sum of bases, and base saturation) and ADJ (Al, potential acidity, Al saturation, B, and Fe) soils. These results contribute to a deeper view of the fungi communities in ADE and open new perspectives for entomopathogenic fungi studies.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-015-0703-7) contains supplementary material, which is available to authorized users.
PMCID: PMC4823338  PMID: 26585119
18S rRNA; Anthrosols; Biochar; Microbial ecology; Pre-Columbian soil; Pyrosequencing
22.  Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment 
Microbial Ecology  2015;71:207-220.
Fungus-growing termites (subfamily Macrotermitinae) mix plant forage with asexual spores of their plant-degrading fungal symbiont Termitomyces in their guts and deposit this blend in fungus comb structures, within which the plant matter is degraded. As Termitomyces grows, it produces nodules with asexual spores, which the termites feed on. Since all comb material passes through termite guts, it is inevitable that gut bacteria are also deposited in the comb, but it has remained unknown which bacteria are deposited and whether distinct comb bacterial communities are sustained. Using high-throughput sequencing of the 16S rRNA gene, we explored the bacterial community compositions of 33 fungus comb samples from four termite species (three genera) collected at four South African geographic locations in 2011 and 2013. We identified 33 bacterial phyla, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Candidate division TM7 jointly accounting for 92 % of the reads. Analyses of gut microbiotas from 25 of the 33 colonies showed that dominant fungus comb taxa originate from the termite gut. While gut communities were consistent between 2011 and 2013, comb community compositions shifted over time. These shifts did not appear to be due to changes in the taxa present, but rather due to differences in the relative abundances of primarily gut-derived bacteria within fungus combs. This indicates that fungus comb microbiotas are largely termite species-specific due to major contributions from gut deposits and also that environment affects which gut bacteria dominate comb communities at a given point in time.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-015-0692-6) contains supplementary material, which is available to authorized users.
PMCID: PMC4686563  PMID: 26518432
Macrotermitinae; Microbiota; Termitomyces; 16S rRNA sequencing; Symbiosis
23.  Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation 
Microbial Ecology  2015;71:616-627.
Here, we investigated how different plant biomass, and—for one substrate—pH, drive the composition of degrader microbial consortia. We bred such consortia from forest soil, incubated along nine aerobic sequential - batch enrichments with wheat straw (WS1, pH 7.2; WS2, pH 9.0), switchgrass (SG, pH 7.2), and corn stover (CS, pH 7.2) as carbon sources. Lignocellulosic compounds (lignin, cellulose and xylan) were best degraded in treatment SG, followed by CS, WS1 and WS2. In terms of composition, the consortia became relatively stable after transfers 4 to 6, as evidenced by PCR-DGGE profiles obtained from each consortium DNA. The final consortia differed by ~40 % (bacteria) and ~60 % (fungi) across treatments. A ‘core’ community represented by 5/16 (bacteria) and 3/14 (fungi) bands was discerned, next to a variable part. The composition of the final microbial consortia was strongly driven by the substrate, as taxonomically-diverse consortia appeared in the different substrate treatments, but not in the (WS) different pH one. Biodegradative strains affiliated to Sphingobacterium kitahiroshimense, Raoultella terrigena, Pseudomonas putida, Stenotrophomonas rhizophila (bacteria), Coniochaeta ligniaria and Acremonium sp. (fungi) were recovered in at least three treatments, whereas strains affiliated to Delftia tsuruhatensis, Paenibacillus xylanexedens, Sanguibacter inulus and Comamonas jiangduensis were treatment-specific.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-015-0683-7) contains supplementary material, which is available to authorized users.
PMCID: PMC4788684  PMID: 26487437
Plant biomass; Bioconversion; Bacterial–fungal consortia; (Hemi) cellulolytic activity
24.  Species Composition of Bacterial Communities Influences Attraction of Mosquitoes to Experimental Plant Infusions 
Microbial ecology  2009;59(1):158-173.
In the container habitats of immature mosquitoes, catabolism of plant matter and other organic detritus by microbial organisms produces metabolites that mediate the oviposition behavior of Aedes aegypti and Aedes albopictus. Public health agencies commonly use oviposition traps containing plant infusions for monitoring populations of these mosquito species, which are global vectors of dengue viruses. In laboratory experiments, gravid females exhibited significantly diminished responses to experimental infusions made with sterilized white oak leaves, showing that attractive odorants were produced through microbial metabolic activity. We evaluated effects of infusion concentration and fermentation time on attraction of gravid females to infusions made from senescent bamboo or white oak leaves. We used plate counts of heterotrophic bacteria, total counts of 4′,6-diamidino-2-phenylindole-stained bacterial cells, and 16S ribosomal DNA (rDNA) polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) to show that changes in the relative abundance of bacteria and the species composition of bacterial communities influenced attraction of gravid A. aegypti and A. albopictus mosquitoes to infusions. DGGE profiles showed that bacterial species composition in infusions changed over time. Principal components analysis indicated that oviposition responses to plant infusions were in general most affected by bacterial diversity and abundance. Analysis of bacterial 16S rDNA sequences derived from DGGE bands revealed that Proteo-bacteria (Alpha-, Beta-, Delta-, and Gamma-) were the predominant bacteria detected in both types of plant infusions. Gravid A. aegypti were significantly attracted to a mix of 14 bacterial species cultured from bamboo leaf infusion. The oviposition response of gravid mosquitoes to plant infusions is strongly influenced by abundance and diversity of bacterial species, which in turn is affected by plant species, leaf biomass, and fermentation time.
PMCID: PMC4561554  PMID: 19641948
25.  The First Record for the Americas of Loxodes rex, a Flagship Ciliate with an Alleged Restricted Biogeography 
Microbial Ecology  2015;71:5-8.
As the foundations of food webs, protozoa are essential to the success of an ecological system. These organisms are often overlooked, and research in the Americas is sparse. Recent samplings conducted in freshwater canals and ponds in Florida, USA, have revealed Loxodes rex, an alleged endemic ciliate species. Originally described as endemic to tropical Africa, L. rex has been considered a prime candidate for proof of microbial endemism. Our studies have shown this giant, non-encysting ciliate to be thriving in subtropical Florida. Our observations are novel and include both the first record of occurrence for the Americas and the first high-quality in vivo images for this charismatic species.
PMCID: PMC4686552  PMID: 26687489
Biogeography; Ciliate; Endemism; Florida; Loxodes rex; Protozoa

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