The Diversity and Distribution of Fungi on Residential Surfaces

The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfaces. To test the fungal aspect of this hypothesis, we sampled fungi from three surface types likely to support growth and therefore possible contributors of fungi to indoor air: drains in kitchens and bathrooms, sills beneath condensation-prone windows, and skin of human inhabitants. Sampling was done in replicated units of a university-housing complex without reported mold problems, and sequences were analyzed using both QIIME and the new UPARSE approach to OTU-binning, to the same result. Surfaces demonstrated a mycological profile similar to that of outdoor air from the same locality, and assemblages clustered by surface type. “Weedy” genera typical of indoor air, such as Cladosporium and Cryptococcus, were abundant on sills, as were a diverse set of fungi of likely outdoor origin. Drains supported more depauperate assemblages than the other surfaces and contained thermotolerant genera such as Exophiala, Candida, and Fusarium. Most surprising was the composition detected on residents’ foreheads. In addition to harboring Malassezia, a known human commensal, skin also possessed a surprising richness of non-resident fungi, including plant pathogens such as ergot (Claviceps purperea). Overall, fungal richness across indoor surfaces was high, but based on known autecologies, most of these fungi were unlikely to be growing on surfaces. We conclude that while some endogenous fungal growth on typical household surfaces does occur, particularly on drains and skin, all residential surfaces appear – to varying degrees – to be passive collectors of airborne fungi of putative outdoor origin, a view of the origins of the indoor microbiome quite different from bacteria.     

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil

Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.     

Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances

The indoor microbiome is a complex system that is thought to depend on dispersal from the outdoor biome and the occupants'' microbiome combined with selective pressures imposed by the occupants'' behaviors and the building itself. We set out to determine the pattern of fungal diversity and composition in indoor air on a local scale and to identify processes behind that pattern. We surveyed airborne fungal assemblages within 1-month time periods at two seasons, with high replication, indoors and outdoors, within and across standardized residences at a university housing facility. Fungal assemblages indoors were diverse and strongly determined by dispersal from outdoors, and no fungal taxa were found as indicators of indoor air. There was a seasonal effect on the fungi found in both indoor and outdoor air, and quantitatively more fungal biomass was detected outdoors than indoors. A strong signal of isolation by distance existed in both outdoor and indoor airborne fungal assemblages, despite the small geographic scale in which this study was undertaken (<500 m). Moreover, room and occupant behavior had no detectable effect on the fungi found in indoor air. These results show that at the local level, outdoor air fungi dominate the patterning of indoor air. More broadly, they provide additional support for the growing evidence that dispersal limitation, even on small geographic scales, is a key process in structuring the often-observed distance–decay biogeographic pattern in microbial communities.     

Dynamics of Bacterial and Fungal Communities on Decaying Salt Marsh Grass

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

Soil Microbial Diversity in the Vicinity of Desert Shrubs

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0–10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon–Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.     

Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth''s extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.     

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

Relating belowground microbial composition to the taxonomic,phylogenetic, and functional trait distributions of trees in a tropical forest

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot‐level variability in belowground microbial communities.     

Resilience to fire of phylogenetic diversity across biological domains

Fire alters the structure and composition of above‐ and belowground communities with concurrent shifts in phylogenetic diversity. The inspection of postfire trends in the diversity of ecological communities incorporating phylogenetic information allows to better understand the mechanisms driving fire resilience. While fire reduces plant phylogenetic diversity based on the recruitment of evolutionarily related species with postfire seed persistence, it increases that of soil microbes by limiting soil resources and changing the dominance of competing microbes. Thus, during postfire community reassembly, plant and soil microbes might experience opposing temporal trends in their phylogenetic diversity that are linked through changes in the soil conditions. We tested this hypothesis by investigating the postfire evolution of plant and soil microbial (fungi, bacteria and archaea) communities across three 20‐year chronosequences. Plant phylogenetic diversity increased with time since fire as pioneer seeders facilitate the establishment of distantly related late‐successional shrubs. The postfire increase in plant phylogenetic diversity fostered plant productivity, eventually recovering soil organic matter. These shifts over time in the soil conditions explained the postfire restoration of fungal and bacterial phylogenetic diversity, which decreased to prefire levels, suggesting that evolutionarily related taxa with high relative fitness recover their competitive superiority during community reassembly. The resilience to fire of phylogenetic diversity across biological domains helps preserve the evolutionary history stored in our ecosystems.     

Airborne bacteria, fungi, and endotoxin levels in residential microenvironments: a case study

Limited data are currently available on the concentrations of airborne bacteria, fungi, and endotoxins in indoor environments. The levels of aerial bacteria and fungi were measured at several microenvironments within a well-ventilated residential apartment in Singapore including the living room, kitchen, bedroom, toilet, and at a workplace environment by sampling indoor air onto culture medium plates using the 6-stage Andersen sampler. Total microbial counts were determined by collecting the air samples in water with the Andersen sampler, staining the resultant extracts with a fluorescent dye, acridine orange, and counting the microbes using a fluorescent microscope. The levels of airborne endotoxins were also determined by sampling the airborne microorganisms onto 0.4?μm polycarbonate membrane filter using the MiniVol sampler at 5?l/min for 20?h with a PM_2.5 cut-off device. The aerial bacterial and fungal concentrations were found to be in the ranges of 117–2,873?CFU/m³ and 160–1,897?CFU/m³, respectively. The total microbial levels ranged from 49,000 to 218,000?microbes/m³. The predominant fungi occurring in the apartment were Aspergillus and Penicillium while the predominant bacterial strains appeared to be Staphylococcus and Micrococcus. The average indoor endotoxin level was detectable in the range of 6–39?EU/m³. The amount of ventilation and the types of human activities carried out in the indoor environment appeared to be important factors affecting the level of these airborne biological contaminants.     

The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ)

We studied prokaryotic community structure and composition in biological soil crusts (BSCs) from the Sonoran Desert, and their variability over space and time, using statistically analyzed, PCR-based molecular surveys of environmental 16S rRNA genes. Four sites, tens of km apart, were sampled, 3 times over a 1 year period, collecting 10 duplicate samples every 50 m in each site. Denaturing gradient gel electrophoresis (DGGE) revealed communities much less diverse than those of typical soil assemblages, displaying dominance of some bacterial types. No differences in crust microbial diversity or composition were detected between crusts under plant canopies and those in plant interspaces, indicating a likely crust independence from higher plant resources. However, statistically significant variability with space and time could be detected, and samples within a site were more similar than samples between sites. Both temporal and spatial variability in community composition involved non-dominant members of the community. Extensive sequencing and phylogenetic analysis revealed a large array of bacterial types, many novel. The most common included members of Cyanobacteria, Proteobacteria, Actinobacteria and Acidobacteria. Bacteriodetes, Chloroflexi and Gemmatimonadetes were not seen in high numbers, but were present in all sites, and Deinococci were also detected. Archaea were present, but as minor components. Sonoran BSC communities were distinct in rough compositional character from those in bulk arid soils or agricultural soils, and contained reoccurring, uncultured microbes.     

Strain differentiation of airborne opportunistic microorganisms within a municipal landfill area as assessed by PCR MP method

A municipal landfill is the site where occurs differentiation of microorganisms inclusive of several hazardous to human health. The aim of this study was to evaluate by a PCR melting profile (PCR MP) technique the level of genetic intraspecies relatedness of strains, representing several opportunistic bacteria and fungi commonly found in bioaerosol in the landfill site. In total, 27 strains representing four bacterial species (i.e. Escherichia coli, Proteus mirabilis, Staphylococcus sciurii, S. xylosus) and 36 fungal strains belonging to Aspergillus fumigatus and A. flavus were isolated from air samples collected by an Anderson impactor within the landfill area. The PCR melting profile approach clearly indicated that except E. coli, represented by one genotype, other microbial species underwent significant genetic variability in the active sector and surrounding the landfill forest and field areas. Although the genetic relatedness of some strains could testify to distribution of microbes from the active sector to the surroundings in the past, the bacterial and fungal isolates indicated site-specific genetic fingerprints. This is the first report on the distribution of airborne opportunistic microbial species within the landfill area, performing a comparison of their genotypes and evaluation of genetic relatedness between the isolates using the PCR MP method.     

Particle size distribution of cultivable airborne microbes and inhalable particulate matter in a wastewater treatment plant facility

A field study was performed to identify the size distribution characteristics of viable, cultivable airborne microorganisms (heterotrophic bacteria, fungi, and total coliforms) at a municipal wastewater treatment facility, and their association with inhalable particulate matter (PM₁, PM_2.5, and PM₁₀), as well as hydrogen sulfide concentrations and ambient meteorological parameters. The highest concentrations of cultivable, airborne heterotrophic bacteria, total coliforms, mass and number concentration of particulate matter, as well as hydrogen sulfide were observed at the aerated grit removal chambers at the pretreatment stage (3 to 2030 times higher than the values of the background ambient air). In contrast, the mean concentrations of cultivable, airborne mesophilic fungi at the aerated grit chambers were 0.6 time lower than the background site, where fungi presented the most abundant taxonomic group in the ambient air. Although the highest concentrations of the airborne fungi were determined at aerodynamic diameters between 2.1 and 3.3 μm, a nearly equal distribution of the mean concentrations of the cultivable, airborne heterotrophic bacteria were observed in the six different size fractions at the primary settling tanks and in the ambient air. Interestingly, their size distribution profiles at the aerated grit chambers were different and showed a maximum aerodynamic diameter at the size range from 3.3 to 4.7 μm, similar to that of the cultivable, airborne total coliforms. In general, low positive or no significant linear relationships could be found between the cultivable airborne heterotrophic bacteria, total coliforms, or fungi at the two wastewater treatment stages and the ambient background microbial community.     

Dynamics of bacterial and fungal communities on decaying salt marsh grass

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

青岛市秋季空气微生物群落多样性

采用KC-6120空气综合采样器采集空气微生物样品,通过构建16S/18SrDNA克隆文库方法分析青岛市市区街道秋季空气微生物群落结构特征.结果表明： 空气细菌分布在6大类,分别为变形菌门(78.8%)、厚壁菌门(14.6%)、放线菌门(4.0%)、浮霉菌门(1.3%)、蓝藻门(0.7%)和栖热菌门(0.6%),优势菌属为不动杆菌属(39.7%)、葡萄球菌属(11.3%)、鞘脂单胞菌属(8.6%)和副球菌属(6.0%).空气真菌分布在子囊菌门(97.5%)和担子菌门(2.5%),优势菌属为核腔菌属(76.5%)、炭角菌属(13.6%)和外瓶霉属(2.5%).空气微生物中存在不动杆菌属、鞘脂单胞菌、葡萄球菌等致病菌或条件致病菌,以及引发多种农作物枯萎死亡的麦类核腔菌、团炭角菌和角状平脐疣孢等真菌.     

Bioaerosols and Particle Release During Composting of Contaminated Sawmill Soil

Compost windrows for bioremediation of soil were built at a wood-preserving site contaminated with chlorophenols, polychlorinated dibenzo-p-dioxins (PCDDs), and polychlorinated dibenzofurans (PCDFs). Sampling of airborne particles during the mixing of the compost windrows found concentrations of PCDDs and PCDFs in different particle sizes. The congener distribution of PCDDs and PCDFs in the collected air particle fractions was similar to that in the compost windrows, and the level of PCDDs and PCDFs was 1000-fold higher than the atmospheric background values reported previously. Viable particle-sizing samplers and several selective growth media were used to enumerate bacteria and fungi in the airborne particles. From the collected air samples, 40 bacteria were isolated and identified. Among the isolated bacteria, 80% were Gram-positive and spore-forming. Two of the identified airborne bacteria, Pseudomonas aeruginosa and Bacillus cereus, may cause human disease and are classified in biological agent hazard group 2. The amounts of airborne fungi, molds, and yeasts were 1000 to 2000 colony-forming units (CFUs) per m³. The number of actinomycetes was up to 6-fold, and the number of bacteria was 2- to 20-fold compared to background values. The overall level of airborne bacteria (200 to 3500 CFUs per m³) was low compared to the level of bacteria (10⁵ to 10⁸ CFUs per m³) found when composting municipal waste.     

青岛市秋季空气微生物群落多样性

采用KC-6120空气综合采样器采集空气微生物样品,通过构建16S/18SrDNA克隆文库方法分析青岛市市区街道秋季空气微生物群落结构特征.结果表明： 空气细菌分布在6大类,分别为变形菌门(78.8%)、厚壁菌门(14.6%)、放线菌门(4.0%)、浮霉菌门(1.3%)、蓝藻门(0.7%)和栖热菌门(0.6%),优势菌属为不动杆菌属(39.7%)、葡萄球菌属(11.3%)、鞘脂单胞菌属(8.6%)和副球菌属(6.0%).空气真菌分布在子囊菌门(97.5%)和担子菌门(2.5%),优势菌属为核腔菌属(76.5%)、炭角菌属(13.6%)和外瓶霉属(2.5%).空气微生物中存在不动杆菌属、鞘脂单胞菌、葡萄球菌等致病菌或条件致病菌,以及引发多种农作物枯萎死亡的麦类核腔菌、团炭角菌和角状平脐疣孢等真菌.     

The air spora of an orchid greenhouse

The orchid collection of the ELTE Botanical Garden, Budapest, Hungary was monitored for airborne fungi using viable and non-viable air-sampling methods (Hirst-type and a 3-stage Andersen sampler) with three different culture media. A new culture method was also applied to identify fungal spores from Hirst-type samples. The aim of this study was to determine the diversity, human- and phytopathological potential of the air spora. To find out sources of airborne fungi, samples were collected from the air in an adjacent greenhouse and outdoors, and from necrotic plants. A total of 58 genera were found in the air samples. Cladosporium and Penicillium spp. were common members of the airborne biota. A high proportion (27.5%) of identified genera may be presented as a member of microbial consortium associated with the orchids. Airborne fungi potentially pathogenic to humans were also detected. One species, Zygosporium masonii, was new to Hungary. Statistical analysis indicated that conditions of sampling had significant effects. The principal component analysis elucidated the three principal components representing 75.34% of the total variance; the clusters of variables were related to the three types of culture media. Relative abundance of small-sized spores was high, presumably because of the fungal species composition and accelerated sedimentation of large spores in still air. Apparently, in the studied orchid greenhouse, a specific mycobiota developed due to the climate and hosts (Orchideaceae) grown there.     

The microbial signature of aerosols produced during the thermophilic phase of composting

Aims:  The microbial diversity of bioaerosols released during operational activities at composting plants is poorly understood. Identification of bacteria and fungi present in such aerosols is the prerequisite for the definition of microbial indicators that could be used in dispersal and exposure studies.
Methods and Results:  A culture-independent analysis of composting bioaerosols collected at five different industrial open sites during the turning of composting piles in fermentation was performed by building 16S rDNA and 18S rDNA libraries. More than 800 sequences were analysed. Although differences in the phylotypes distribution were observed from one composting site to another, similarities in the structure of microbial diversity were remarkable. The same phyla dominated in the five bioaerosols: Ascomycota among fungi, Firmicutes and Actinobacteria among bacteria. For each phylum, some dominant phylotypes were common to at least four bioaerosols. These common phylotypes belonged to Thermomyces , Aspergillus , Penicillium , Geobacillus, Planifilum , Thermoactinomyces , Saccharopolyspora , Thermobifida and Saccharomonospora .
Conclusions:  The microbial signature of aerosols produced during the thermophilic phase of composting was determined. The similarities observed may be explained by the selection of thermophilic and sporulating species.
Significance and Impact of the Study:  Several bacteria and fungi identified in this study may represent potential indicators of composting bioaerosols in air.