Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

BackgroundThe study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building.ResultsIndoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative abundance of tap water-derived microorganisms in air.ConclusionsIndoor air in residences harbors a diverse bacterial community originating from both outdoor and indoor sources and is strongly influenced by household characteristics

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

Development of a biomarker for Geobacter activity and strain composition: Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)

Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes

Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

BackgroundThe study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building.ResultsIndoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative abundance of tap water-derived microorganisms in air.ConclusionsIndoor air in residences harbors a diverse bacterial community originating from both outdoor and indoor sources and is strongly influenced by household characteristics

El defensor : Diario Liberal independiente, protector de los intereses materiales y morales de esta provincia: Año III Epoca segunda Número 428 - 1905 julio 19

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Additional file 1: Table S1. of Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences

OTU table. Genus-level taxonomic composition of bacterial communities associated with indoor air and sources. Columns correspond to samples, rows correspond to OTUs, and values represent the number of times an OTU appears in a particular sample. (xlsx 684 kb

Additional file 5: Table S4. of Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences

Metadata associated with all residences sampled in this study. Information on the characteristics of the household was collected at the time of sampling. (xlsx 12.1 kb

Additional file 3: Figures S1-S4. Figure S1 of Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences

Principal coordinate plot showing the overall variation in bacterial community composition in indoor air and sources. Indoor air bacterial communities in homes (large open circles) show various degrees of overlapping with outdoor-related source environments (closed circles), indoor-related source environments (crosses), and water-related source environments (open circles). Differences in the composition of the bacterial communities were quantified using the weighted UniFrac distance metric and symbols closer together indicate samples with more similar bacterial communities. Figure S2. Relationship between weighted and unweighted UniFrac phylogenetic distance (ANOSIM R) between microbial communities in indoor air and different source environments. R values close to 0 indicate similarity between indoor air microbial communities and the sources; the opposite is true for R values close to 1. The statistical significance (p) of the correlation was determined using Spearman’s rank correlation coefficient (ρ). Figure S3. Sink prediction (SourceTracker) in indoor air and weighted UniFrac phylogenetic distance (ANOSIM R) with indoor air for microbial communities in different source environments. Higher sink prediction values for a source environment indicate a higher proportion of its OTUs in indoor air. R values close to 0 indicate similarity between indoor air microbial communities and the sources; the opposite is true for R values close to 1. The statistical significance (p) of the correlation was determined using Spearman’s rank correlation coefficient (ρ). Figure S4. Correlation between the taxonomic distance and geographic distance for indoor air (a) and outdoor air (b) bacterial communities. The taxonomic distance was determined using weighted UniFrac metrics. The statistical significance was determined using the Mantel r statistics (999 permutations). (PDF 281 kb