Microbial community related to volatile organic compound (VOC) emission in household biowaste

Malodorous emissions and potentially pathogenic microorganisms which develop during domestic organic waste collection are not only a nuisance but may also pose health risks. The aim of the present study was to determine whether the presence of specific microorganisms in biowastes is directly related to the composition of the emitted volatile organic compounds (VOCs). The succession of microbial communities during 16 days of storage in organic waste collection bins was studied by denaturing gradient gel electrophoresis (DGGE) of amplified 16S ribosomal DNA in parallel with a classical cultivation and isolation approach. Approximately 60 different bacterial species and 20 different fungal species were isolated. Additionally, some bacterial species were identified through sequencing of excised DGGE bands. Proton transfer reaction mass spectrometry (PTR-MS) was used to detect VOCs over the sampling periods, and co-inertia analyses of VOC concentrations with DGGE band intensities were conducted. Positive correlations, indicating production of the respective VOC or enhancement of microbial growth, and negative correlations, indicating the use of, or microbial inhibition by the respective compound, were found for the different VOCs. Measurement of the VOC emission pattern from a pure culture of Lactococcus lactis confirmed the positive correlations for the protonated masses 89 (tentatively identified as butyric acid), 63 (tentatively identified as dimethylsulfide), 69 (likely isoprene) and 73 (likely butanone).     

Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters

AIMS: To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air. METHODS AND RESULTS: A microbiological study and a measurement of biodegradation activities were simultaneously carried out on two identical peat-packed columns, seeded with two different inocula, treating polluted air containing 11 VOCs. For both reactors, the spatial structure of the microbial communities was investigated by means of single-strand conformation polymorphism (SSCP) analysis. For both reactors, stratification of degradation activities in function of depth was observed. Oxygenated compounds were removed at the top of the column and aromatics at the bottom. Comparison of SSCP patterns clearly showed a shift in community structure in function of depth inside both biofilters. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. Although the operating conditions of both reactors were identical and the biodegradation activities similar, the composition of microflora differed for biofilters A and B. Subdivision of biofilter B into two independent parts supplied with polluted air containing the complex VOC mixture showed that the microflora having colonized the bottom of biofilter B retained their potential for degrading oxygenated compounds. CONCLUSIONS: This work highlights the spatialization of biodegradation functions in a biofilter treating a complex mixture of VOCs. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: This vertical structure of microbial communities must be taken into consideration when dealing with the malfunctioning of bioreactors. These results are also useful information about changes in microbial communities following natural or anthropogenic alterations in different ecosystems (soils and sediments) where structuring of microbial communities according to depth has been observed.     

Reintroduction of locally extinct vertebrates impacts arid soil fungal communities

Introduced species have contributed to extinction of native vertebrates in many parts of the world. Changes to vertebrate assemblages are also likely to alter microbial communities through coextinction of some taxa and the introduction of others. Many attempts to restore degraded habitats involve removal of exotic vertebrates (livestock and feral animals) and reintroduction of locally extinct species, but the impact of such reintroductions on microbial communities is largely unknown. We used high‐throughput DNA sequencing of the fungal internal transcribed spacer I (ITS1) region to examine whether replacing exotic vertebrates with reintroduced native vertebrates led to changes in soil fungal communities at a reserve in arid central Australia. Soil fungal diversity was significantly different between dune and swale (interdune) habitats. Fungal communities also differed significantly between sites with exotic or reintroduced native vertebrates after controlling for the effect of habitat. Several fungal operational taxonomic units (OTUs) found exclusively inside the reserve were present in scats from reintroduced native vertebrates, providing a direct link between the vertebrate assemblage and soil microbial communities. Our results show that changes to vertebrate assemblages through local extinctions and the invasion of exotic species can alter soil fungal communities. If local extinction of one or several species results in the coextinction of microbial taxa, the full complement of ecological interactions may never be restored.     

Indoor-Biofilter Growth and Exposure to Airborne Chemicals Drive Similar Changes in Plant Root Bacterial Communities

Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genus Hyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains of Hyphomicrobium proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.     

Lichen diversity on stumps in relation to wood decay in subalpine forests of Northern Italy

Although several studies demonstrated the importance of dead wood for lichen conservation in N-Europe and N-America, the lichen biota on dead wood was poorly studied in the Alps, where stumps represent one of the main available dead wood type. This work aims at evaluating species richness and composition of lichens in relation to the decay of stumps in subalpine forests of the Italian Alps. Differences in species richness between three decay stages were tested using a one-way ANOVA, while the pattern of species composition was evaluated with non-metric multidimensional scaling and an Indicator Species Analysis. Overall, 69 species were found and wood decay proved to be an important factor influencing lichen communities on stumps in our subalpine forests. Despite the fact that the mean number of species per stump did not differ between the three decay stages and lichen communities broadly overlapped, a main pattern of species turnover was identified across wood decay process as well as some indicator species for each decay stage. During the decay process, lichen communities change functional and ecological composition as an adaptive response to the continuous change of substrate. Since stumps host several nationally rare species, which are related to different stages of decay, they could have a relevant role in lichen conservation in managed forests where other types of dead wood are normally absent.     

Distance decay of similarity among parasite communities of three marine invertebrate hosts

The similarity in species composition between two communities generally decays as a function of increasing distance between them. Parasite communities in vertebrate definitive hosts follow this pattern but the respective relationship in intermediate invertebrate hosts of parasites with complex life cycles is unknown. In intermediate hosts, parasite communities are affected not only by the varying vagility of their definitive hosts (dispersing infective propagules) but also by the necessary coincidence of all their hosts in environmentally suitable localities. As intermediate hosts often hardly move they do not contribute to parasite dispersal. Hence, their parasite assemblages may decrease faster in similarity with increasing distance than those in highly mobile vertebrate definitive hosts. We use published field survey data to investigate distance decay of similarity in trematode communities from three prominent coastal molluscs of the Eastern North-Atlantic: the gastropods Littorina littorea and Hydrobia ulvae, and the bivalve Cerastoderma edule. We found that the similarity of trematode communities in all three hosts decayed with distance, independently of local sampling effort, and whether or not the parasites used the mollusc as first or second intermediate host in their life cycle. In H. ulvae, the halving distance (i.e. the distance that halves the similarity from its initial similarity at 1 km distance) for the trematode species using birds as definitive hosts was approximately two to three times larger than for species using fish. The initial similarities (estimated at 1 km distance) among trematode communities were relatively higher, whereas mean halving distances were lower, compared to published values for parasite communities in vertebrate hosts. We conclude that the vagility of definitive hosts accounts for a high similarity at the local scale, while the strong decay of similarity across regions is a consequence of the low probability that all necessary hosts and suitable environmental conditions coincide on a large scale.     

Volatile Compounds Originating from Mixed Microbial Cultures on Building Materials under Various Humidity Conditions

We examined growth of mixed microbial cultures (13 fungal species and one actinomycete species) and production of volatile compounds (VOCs) in typical building materials in outside walls, separating walls, and bathroom floors at various relative humidities (RHs) of air. Air samples from incubation chambers were adsorbed on Tenax TA and dinitrophenylhydrazine cartridges and were analyzed by thermal desorption-gas chromatography and high-performance liquid chromatography, respectively. Metabolic activity was measured by determining CO₂ production, and microbial concentrations were determined by a dilution plate method. At 80 to 82% RH, CO₂ production did not indicate that microbial activity occurred, and only 10% of the spores germinated, while slight increases in the concentrations of some VOCs were detected. All of the parameters showed that microbial activity occurred at 90 to 99% RH. The microbiological analyses revealed weak microbial growth even under drying conditions (32 to 33% RH). The main VOCs produced on the building materials studied were 3-methyl-1-butanol, 1-pentanol, 1-hexanol, and 1-octen-3-ol. In some cases fungal growth decreased aldehyde emissions. We found that various VOCs accompany microbial activity but that no single VOC is a reliable indicator of biocontamination in building materials.     

Plant metabolomics for plant chemical responses to belowground community change by climate change

General circulation models on global climate change predict increase in surface air temperature and changes in precipitation. Increases in air temperature (thus soil temperature) and altered precipitation are known to affect the species composition and function of soil microbial communities. Plant roots interact with diverse soil organisms such as bacteria, protozoa, fungi, nematodes, annelids and insects. Soil organisms show diverse interactions with plants (eg. competition, mutualism and parasitism) that may alter plant metabolism. Besides plant roots, various soil microbes such as bacteria and fungi can produce volatile organic compounds (VOCs), which can serve as infochemicals among soil organisms and plant roots. While the effects of climate change are likely to alter both soil communities and plant metabolism, it is equally probable that these changes will have cascading consequnces for grazers and subsequent food web components aboveground. Advances in plant metabolomics have made it possibile to track changes in plant metabolomes as they respond to biotic and abiotic environmental changes. Recent developments in analytical instrumentation and bioinformatics software have established metabolomics as an important research tool for studying ecological interactions between plants and other organisms. In this review, we will first summarize recent progress in plant metabolomics methodology and subsequently review recent studies of interactions between plants and soil organisms in relation to climate change issues.     

Microbial consumption and production of volatile organic compounds at the soil-litter interface

Substantial amounts of volatile organic compounds (VOCs) can be released during decomposition and these compounds can affect atmospheric chemistry, belowground processes, and the structure of microbial communities in litter and soil. However, we have a limited understanding of the types, quantities and ecological impacts of VOCs emitted from litter. Here we used a closed flow-through system and proton transfer reaction mass spectrometry (PTR-MS) to characterize VOC emissions from soil and two litter types (Pinus taeda and Acer rubrum) over a 72-day incubation period. Microbial respiration rates were measured throughout the incubation, and the soils were harvested at the end of the incubation to determine how litter VOCs influenced soil C dynamics, N mineralization rates, and bacterial communities. Using the PTR-MS we identified over 100 VOCs, with 10 VOCs making up the majority of emissions. VOCs accounted for up to 2.5% of the C flux from litter. Soil was a net sink of litter VOCs, absorbing up to 80% of VOCs released by litter, and exposure of soil to litter VOCs increased microbial respiration rates in soil by up to 15%. However, we observed negligible impacts of litter VOCs on soil nutrient levels and bacterial community structure, suggesting that soils must be exposed to higher concentrations of VOCs than observed in our study, to cause effects on these soil characteristics. Overall, VOCs appear to have an important influence on C dynamics at the soil-litter interface and VOC emissions from decomposing litter may represent an understudied component of biosphere–atmosphere interactions.     

Structural and functional responses of sewage microbial communities used for the treatment of a complex mixture of volatile organic compounds (VOCs)

Aims:  The aim of this work was to assess the impact of the applied mass loading on the selection of an efficient microbial community able to degrade a complex mixture of volatile organic compounds (VOCs).
Methods and Results:  Two reactors were used and were supplied with a gaseous effluent containing 11 VOCs with different concentrations. The response of the microflora was monitored as a function of time: biodegradation activity, bacterial density and diversity. The results showed that the applied mass loading seems to have an impact on the functioning and the genetic structure of the bacterial community.
Conclusions:  A high mass loading seems to induce a low efficient functioning in terms of elimination efficiency and a simplification of the genetic structure of the total bacterial community with the apparition of a dominant microflora. A low mass loading seems to favour a better functioning and allows to keep a healthier bacterial diversity.
Significance and Impact of the Study:  In the treatment processes of gaseous effluents, it would be judicious to define the functioning parameters of the process to keep the diversity of important functional bacterial groups. These results provide also useful information about changes in microbial communities following natural or anthropogenic alterations in different ecosystems.     

Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

Microbes are transported in hydrological networks through many environments, but the nature and dynamics of underlying microbial metacommunities and the impact of downslope inoculation on patterns of microbial diversity across landscapes are unknown. Pyrosequencing of small subunit ribosomal RNA gene hypervariable regions to characterize microbial communities along a hydrological continuum in arctic tundra showed a pattern of decreasing diversity downslope, with highest species richness in soil waters and headwater streams, and lowest richness in lake water. In a downstream lake, 58% and 43% of the bacterial and archaeal taxa, respectively, were also detected in diverse upslope communities, including most of the numerically dominant lake taxa. In contrast, only 18% of microbial eukaryotic taxa in the lake were detected upslope. We suggest that patterns of diversity in surface waters are structured by initial inoculation from microbial reservoirs in soils followed by a species-sorting process during downslope dispersal of both common and rare microbial taxa. Our results suggest that, unlike for metazoans, a substantial portion of bacterial and archaeal diversity in surface freshwaters may originate in complex soil environments.     

The Temporal Scaling of Bacterioplankton Composition: High Turnover and Predictability during Shrimp Cultivation

The spatial distribution of microbial communities has recently been reliably documented in the form of a distance–similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity–time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P?=?0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w?=?0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO₄ ^3-, and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance–similarity decay model.     

黑土母质熟化过程微生物群落碳源代谢特征

东北黑土区由于表土丧失,母质裸露等问题,严重威胁粮食生产和生态环境,通过揭示母质肥力形成过程中微生物群落的碳源利用特征可以让人们更好的理解肥力形成过程中相关微生物过程。以海伦农田生态系统国家野外科学观测研究站长期定位试验为材料,研究母质不同熟化过程下微生物群落碳源代谢特征,结果表明:苜蓿草熟化过程(PAfl)、农田化肥配施有机物熟化过程(PCS+F+OM)可培养微生物数量最多。自然熟化过程(PNat)、苜蓿草熟化过程、农田化肥农产品全循环熟化过程(PCS+F+BM)、农田化肥加有机肥配合型熟化过程可以将微生物活性提高到常规农田黑土的水平。不同熟化过程下微生物群落对单个碳源的利用不同。主成分分析表明自然熟化过程、农田化肥投入熟化过程(PCS+F)、农田化肥农产品全循环熟化过程、农田化肥加有机肥配合型熟化过程与常规农田黑土微生物代谢特征类似。研究表明不同母质熟化过程通过影响微生物群落结构导致对各个碳源的利用发生变化,最终改变了整体碳源代谢特征。     

凋落物分解过程中土壤微生物群落的变化

凋落物分解是生态系统碳循环和营养物质循环的关键过程, 受多种因素共同影响。土壤微生物是影响凋落物分解的重要因素, 其群落组成在一定程度上依赖于所处植物群落的特征。因此, 研究分解过程中微生物群落组成的变化及其对植物多样性的响应, 有利于对凋落物分解机制的理解。本文采用分解袋野外原位分解的方法, 对凋落物分解过程中微生物群落的变化及其对所处森林环境中树木的种类和遗传多样性的响应进行了研究。结果表明: (1)凋落物分解183天后, 土壤中微生物群落的多样性降低, 并且森林群落的物种多样性与微生物群落多样性呈负相关关系; (2)凋落物分解前后, 土壤中真菌和细菌群落的磷脂脂肪酸(PLFA)量均有所增加, 说明凋落物分解为微生物生存和繁殖提供了养分; (3)地形因素是影响微生物群落变化最显著的因素, 可解释微生物群落变化的29.55%; 其次是凋落物的基质质量, 可以解释15.39%; 最后是森林群落的多样性, 可以解释8.45%; 这3种因素共同解释率为2.97%。综上所述, 与森林群落的植物多样性相比, 样地的地形因素与凋落物的基质质量对微生物群落的影响更显著。     

Growth form rather than phylogenetic relationship predicts broad volatile emission patterns in the Brassicaceae

Volatile organic compounds (VOCs) released from plants are known to mediate indirect defense against herbivores and trigger intra- and interplant signaling. While systemic defense response can be mediated both via volatile and vascular signals, it is not clear whether common ancestry and/or plant growth forms influence the choice of either mode in planta. We hypothesize that larger woody plants with a complex anatomy should rely more on volatile-mediated signaling, apparently to circumvent vascular restrictions that slow down the communication over a large distance. On the other hand, in smaller herbaceous plants faster systemic response can be achieved via vascular signaling. To investigate whether plant VOCs emission is related to plant phylogeny or growth form, we studied the composition of herbivory-induced plant volatiles in 13 Brassicaceae species representing all four evolutionary lineages, because this family is characterized by both a well-resolved phylogeny and highly diverse growth forms. Our results revealed that woody species consistently emitted a more complex blend of volatiles than herbaceous species. However, phylogenetic relatedness of the species did not explain the observed volatile emission patterns. This emphasizes the influence of growth form, rather than phylogenetic relationships on the variation in plant volatile emissions. Our findings suggest that woody, perennial plant species emit diverse VOCs, likely because these compounds comprise a more efficient mode of defense response in these large, anatomically complex plants.     

Fungal volatile organic compounds: A review with emphasis on their biotechnological potential

Fungi produce various mixtures of gas-phase, carbon-based compounds called volatile organic compounds (VOCs) that due to their small size are able to diffuse through the atmosphere and soils. Despite some methodological and technological constraints, researchers have detected and characterized approximately 250 fungal VOCs, many of which have characteristic odors and are produced during primary and secondary metabolism. Fungal VOCs may contribute to a controversial medical diagnosis called “sick building syndrome” and may also be important in the success of some biocontrol species of Trichoderma. VOCs also play important signaling roles for fungi in their natural environments. Many ecological interactions are mediated by VOCs, including those between fungi and plants, arthropods, bacteria, and other fungi. The diverse functions of fungal VOCs can be developed for use in biotechnological applications for biofuel, biocontrol, and mycofumigation. Volatiles represent a new frontier in bioprospecting, and the study of these gas-phase compounds promises the discovery of new products for human exploitation and will generate new hypotheses in fundamental biology.     

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development.     

Microbial compositions and metabolic interactions in one- and two-phase partitioning airlift bioreactors treating a complex VOC mixture

Engineered microbial ecosystems in bioscrubbers for the treatment of volatile organic compounds (VOCs) have been complicated by complex VOC mixtures from various industrial emissions. Microbial associations with VOC removal performance of the bioscrubbers are still not definitive. Here, one- and two-phase partitioning airlift bioreactors were used for the treatment of a complex VOC mixture. Microbial characteristics in both bioreactors were uncovered by high-throughput metagenomics sequencing. Results showed that dominant species with specialized VOC biodegradability were mainly responsible for high removal efficiency of relative individual VOC. Competitive enzyme inhibitions among the VOC mixture were closely related to the deterioration of removal performance for individual VOC. Relative to the mass transfer resistance, the specialized biodegrading functions of microbial inoculations and enzymatic interactions among individual VOC biodegradation also must be carefully evaluated to optimize the treatment of complex VOC mixtures in bioreactors.     

Host recognition by Rhinocyllus conicus of floral scents from invasive and threatened thistles

One of the main obstacles of classical biological control is that biological control organisms cannot be recalled once they are released in nature. It is particularly true for the flowerhead weevil, Rhinocyllus conicus Frölich, which was released as a biological control organism for the invasive musk thistle, Carduus nutans L. (MT). While weevils successfully suppressed introduced populations of musk thistles and other invasive thistle species, non-target attacks have been reported on multiple native thistles including federally listed threatened and endangered (T&E) thistle species. To investigate the foraging behavior of female weevils on invasive and native thistles, we examined volatile organic compounds (VOCs) emitted from MT and a T&E plant species, Sacramento Mountains thistle, Cirsium vinaceum Wooton & Standley (SMT) in the Lincoln National Forest, New Mexico. We used a dynamic headspace volatile collection system and gas chromatography-mass spectrometry to compare volatile profiles between MT and SMT. Female weevils reacted to 7 electrophysiologically active chemical compounds in the blends based on gas chromatography-electroantennography. The behavioral response of female weevils was indifferent when VOCs from both thistles were offered in y-tube olfactometry experiments. Yet, they preferred VOCs collected from MT to purified air. The searching time of female weevils was longer to VOCs collected from SMT over controls. Investigating signals during the initial host recognition of released biological control organisms may open new opportunities to reduce non-target attacks on T&E plant species.

     

Achieving similar root microbiota composition in neighbouring plants through airborne signalling

The ability to recognize and respond to environmental signals is essential for plants. In response to environmental changes, the status of a plant is transmitted to other plants in the form of signals such as volatiles. Root-associated bacteria trigger the release of plant volatile organic compounds (VOCs). However, the impact of VOCs on the rhizosphere microbial community of neighbouring plants is not well understood. Here, we investigated the effect of VOCs on the rhizosphere microbial community of tomato plants inoculated with a plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain GB03 and that of their neighbouring plants. Interestingly, high similarity (up to 69%) was detected in the rhizosphere microbial communities of the inoculated and neighbouring plants. Leaves of the tomato plant treated with strain GB03-released β-caryophyllene as a signature VOC, which elicited the release of a large amount of salicylic acid (SA) in the root exudates of a neighbouring tomato seedling. The exposure of tomato leaves to β-caryophyllene resulted in the secretion of SA from the root. Our results demonstrate for the first time that the composition of the rhizosphere microbiota in surrounding plants is synchronized through aerial signals from plants.Subject terms: Microbial ecology, Soil microbiology