The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni).

Background: Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals. Objectives: In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor. Results: The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species. Conclusions: Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.

Fungal communities in European alpine soils are not affected by short-term in situ simulated warming than bacterial communities.

The impact of global warming on biological communities colonizing European alpine ecosystems was recently studied. Hexagonal open top chambers (OTCs) were used for simulating a short-term in situ warming (estimated around 1°C) in some alpine soils to predict the impact of ongoing climate change on resident microbial communities. Total microbial DNA was extracted from soils collected either inside or outside the OTCs over 3 years of study. Bacterial and fungal rRNA copies were quantified by qPCR. Metabarcoding sequencing of taxonomy target genes was performed (Illumina MiSeq) and processed by bioinformatic tools. Alpha- and beta-diversity were used to evaluate the structure of bacterial and fungal communities. qPCR suggests that, although fluctuations have been observed between soils collected either inside and outside the OTCs, the simulated warming induced a significant (p < 0.05) shift only for bacterial abundance. Likewise, significant (p < 0.05) changes in bacterial community structure were detected in soils collected inside the OTCs, with a clear increase of oligotrophic taxa. On the contrary, fungal diversity of soils collected either inside and outside the OTCs did not exhibit significant (p < 0.05) differences, suggesting that the temperature increase in OTCs compared to ambient conditions was not sufficient to change fungal communities.

Bacterial Succession and Community Dynamics of the Emerging Leaf Phyllosphere in Spring.

Every year, deciduous trees shed their leaves, and when new leaves emerge next spring, they establish a characteristic bacterial leaf community. In this exploratory study, we assessed the bacterial phyllosphere (aboveground plant surfaces) of eight London plane trees (Platanus × acerifolia) in Antwerp and Milan by sampling weekly during leaf emergence and expansion. We sampled the surfaces of different tree compartments: leaves, leaf buds, branches, and trunk, for up to 6 weeks. Phyllosphere community composition was most strongly determined by tree compartment. Only the communities on the emerging leaves showed changing dynamics over time. The rate of change in the leaf phyllosphere composition, expressed as the beta dissimilarity between consecutive time points, was very high following leaf emergence, with decreasing speed over time, indicating that these communities stabilize over time. We also identified cooccurring groups of bacteria associated with potential stages of ecological succession on the leaves and accordingly named them general cluster, early cluster, middle cluster, and late cluster. Taxa of the general cluster were not only more abundant than the others on leaves, but they were also widespread on other tree compartments. The late cluster was most pronounced in trees surrounded by trafficked urban land use. This study mainly generates hypotheses on the ecological succession on the emerging leaves of deciduous trees in urban environments and contributes to understanding the development of the tree leaf phyllosphere in spring. IMPORTANCE Improving our understanding of phyllosphere ecology is key in successfully applying bacterial biological agents or modulating the leaf microbiome in order to achieve valuable ecosystem services, such as plant protection, plant growth, air purification, and developing a healthy human immune system. Modulation of the phyllosphere microbiome in the field works only with variable success. To improve the impact of our applications in the field, a better understanding of the ecological principles governing phyllosphere dynamics is required. This exploratory study demonstrates how the combination of different analyses of a chronosequence of bacterial communities can provide new ecological insights. With a limited number of sampled trees, we demonstrated different indications of ecological succession of bacterial communities in the leaves and observed a potential impact of intensely trafficked land use becoming apparent in the leaf bacterial communities approximately 3 weeks after leaf emergence, consisting of a separate stage in community development.

Integrated biological and chemical characterisation of a pair of leonardesque canal lock gates.

The Museo Nazionale della Scienza e della Tecnologia "Leonardo da Vinci" in Milan is exposing two pairs of canal lock gates, used to control the water flow in Milan canal system, whose design appears in the Leonardo's Codex Atlanticus. The wood present in the gates has been deeply characterised by mean of a multidisciplinary investigation involving i) DNA barcoding of wood fragments; ii) microbial community characterisation, and iii) chemical analyses. DNA barcoding revealed that two fragments of the gates belonged to wood species widely used in the middle age: Fagus sylvatica and Picea abies. The chemical characterisations were based on the use of ionic liquid as dissolving medium in order to analyse the entire cell wall material by means of Gel Permeation Chromatography (GPC) and 2D-NMR-HSQC techniques. This multidisciplinary analytical approach was able to highlight the complex nature of the degradation occurred during the gate operation (XVI-XVIII centuries): an intricate interplay between microbial populations (i.e. Shewanella), inorganic factors (i.e. iron from nails), physical factors and the lignocellulosic material.

Characterization of long-range transported bioaerosols in the Central Mediterranean.

Airborne bacteria were characterized over a 2-y period via high-throughput massive sequencing of 16S rRNA gene in aerosol samples collected at a background mountain European Monitoring and Evaluation Programme (EMEP) Network site (Monte Martano, Italy) located in the Central Mediterranean area. The air mass origin of nineteen samples was identified by air mass modelling and a detailed chemical analysis was performed. Four main origins (Saharan, North-western, North-eastern, and Regional) were identified, and distinct microbial communities were associated with these air masses. Samples featured a great bacterial diversity with Protobacteria being the most abundant phylum, and Sphingomonas followed by Acidovorax, Acinetobacter and Stenotrophomonas the most abundant genera of the dataset. Bacterial genera including potential human and animal pathogens were more abundant in European and in Regional samples compared to Saharan samples; this stressed the relevance of anthropic impact on bacterial populations transported by air masses that cross densely populated areas. The principal aerosol chemical characteristics and the airborne bacterial communities were correlated by cluster analysis, similarity tests and non-metric multidimensional scaling analysis, explaining most of the variability observed. However, the strong correlation between bacterial community structure and air mass origin hampered the possibility to disentangle the effects of variations in bacterial populations and in dust provenance on variations in chemical variables.

Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area.

Plants and phyllosphere microorganisms may effectively contribute to reducing air pollution in cities through the adsorption and biodegradation of pollutants onto leaves. In this work, during all seasons, we sampled atmospheric particulate matter (PM10) and leaves of southern magnolia Magnolia grandiflora and deodar cedar Cedrus deodara, two evergreen plant species widespread in the urban area of Milan where the study was carried out. We then quantified Polycyclic Aromatic Hydrocarbons (PAHs) both in PM10 and on leaves and used sequencing of 16S rRNA gene, shotgun metagenomics and qPCR analyses to investigate the microbial communities hosted by the sampled leaves. Taxonomic and functional profiles of epiphytic bacterial communities differed between host plant species and seasons and the microbial communities on leaves harboured genes involved in the degradation of hydrocarbons. Evidence collected in this work also suggested that the abundance of hydrocarbon-degrading microorganisms on evergreen leaves increased with the concentration of hydrocarbons when atmospheric pollutants were deposited at high concentration on leaves, and that the biodegradation on the phyllosphere can contribute to the removal of PAHs from the urban air.

Cloacal microbiomes and ecology of individual barn swallows.

Microbiomes can be considered as 'second genomes' for the host, and can deeply affect its physiology, behaviour and fitness. We investigated the cloacal microbiomes (CMs) of adult and nestling barn swallows (Hirundo rustica), a small insectivorous migratory passerine bird, in order to assess whether CM structure was related to major ecological traits of individuals. Illumina sequencing of the V5-V6 hypervariable regions of the bacterial 16S rRNA gene showed that barn swallow CMs were dominated by Proteobacteria, Firmicutes, Actinobacteria, Tenericutes and Bacteroidetes. Nestling CMs were more similar to one another than adult ones, but showed higher alpha diversity. Sibling nestlings had more similar CMs than non-sibling ones. CMs of adult males also differed from those of adult females, but pair members had more similar CMs than expected by chance. In contrast, CMs did not differ between male and female nestlings. Finally, in adults, CMs strongly different from the 'average' CM were associated to lower survival prospects of the host. The CMs of a bird species in the wild are therefore related to important traits of individuals, such as survival, suggesting that microbiomes should be included among the traits examined in ecological studies.

Airborne bacteria and persistent organic pollutants associated with an intense Saharan dust event in the Central Mediterranean.

In this paper, we present a comprehensive taxonomic survey of the bacterial community and accurate quantification of polycyclic aromatic hydrocarbons (PAHs) associated with an intense Saharan dust advection, which impacted Central Mediterranean area in the whole 2014-2015 period. This work is part of an intensive field campaign at the EMEP regional background site of Monte Martano (Central Italy), considered well representative of long-range transport in the Central Mediterranean area. 22 samples have been characterized in their provenance region and have been considered for the chemical and biological characterization. The event described in the present paper was exceptionally intense at the sampling site allowing a detailed evaluation of the dust load on a regional scale, an estimation of the impact of PAH based on the Toxic Equivalency Factor methodology and a thorough characterization of the airborne bacterial fraction performed by High Throughput Sequencing approach. Afterward, we cultured viable bacteria and evaluated several enzymatic activities and conducted UV survival tests. Principal findings include: (i) the striking evidence that, during the Saharan dust event, a highly diverse and abundant bacterial community was associated with PAH concentrations higher than the yearly mean; (ii) the tangible presence of cultivable microbes; (iii) the proof that the isolates recovered from Saharan dust had the potential to be metabolically active and that almost all of them were able to persist following UV radiation exposure. Comparisons of results for the present case study with mean values for the 2014-2015 experimental campaign are presented. The bacterial community and chemical speciation associated with the Saharan dust advection were specific and very different from those associated with other air masses. The particular case of North-Western Atlantic, which represents one of the most typical advection route reaching the sampling site is discussed in detail.

Bacteria contribute to pesticide degradation in cryoconite holes in an Alpine glacier.

Organic contaminants deposited on glacier snow and ice are subject to partitioning and degradation processes that determine their environmental fate and, consequently, their accumulation in ice bodies. Among these processes, organic compound degradation by supraglacial bacteria has been investigated to a lesser extent than photo- and chemical degradation. We investigated biodegradation of the organophosphorus insecticide chlorpyrifos (CPF), a xenobiotic tracer that accumulates on glaciers after atmospheric medium- and long-range transport, by installing in situ microcosms on an Alpine glacier to simulate cryoconite hole systems. We found that biodegradation contributed to the removal of CPF from the glacier surface more than photo- and chemical degradation. The high concentration of CPF (2-3 µg g-1 w.w.) detected in cryoconite holes and the estimated half-life of this compound (35-69 days in glacier environment) indicated that biodegradation can significantly reduce CPF concentrations on glaciers and its runoff to downstream ecosystems. The metabolic versatility of cryoconite bacteria suggests that these habitats might contribute to the degradation of a wide class of pollutants. We therefore propose that cryoconite acts as a "biofilter" by accumulating both pollutants and biodegradative microbial communities. The contribution of cryoconite to the removal of organic pollutants should be included in models predicting the environmental fate of these compounds in cold areas.

Influence of seasonality, air mass origin and particulate matter chemical composition on airborne bacterial community structure in the Po Valley, Italy.

The integration of chemical and biological data in aerosol studies represents a new challenge in atmospheric science. In this perspective it will be possible to gain a clearer and deeper comprehension of biogeochemical cycles in the atmosphere. In this view, this study aimed to investigate the relationships occurring between bacterial populations and PM chemical composition in one of the most polluted and urbanized areas in Europe: the Po Valley (Italy). Moreover, seasonality, long- and short-range transports were also evaluated to investigate the influence on airborne bacterial communities. PM samples were collected in two cities of the Po Valley (Milan and Venice) characterized by different meteorological conditions and atmospheric pollutant sources. Samples were analysed for water-soluble inorganic ions (WSIIs) and bacterial community structure. Chemical and biological data were jointly processed by using redundancy discriminate analysis (RDA), while the influence of atmospheric circulation was evaluated by using wind ground data and back-trajectories analysis. Results showed strong seasonal shifts of bacterial community structure in both cities, while a different behaviour was observed for air mass circulation at Milan ad Venice sites: long-range transport significantly affected bacterial populations in Milan whereas local ground wind had more influence in the Venice area. Moreover, difference in taxonomic composition can be mostly addressed to the characteristics of sampling sites. This evidence could suggest that, while PM composition is influenced by long-range transport, bacterial populations are affected, besides transport, by other factors (i.e., season and sampling site location). This perspective allow to better understand and explain airborne bacterial community behaviour.

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier.

We investigated the potential contribution of ice-marginal environments to the microbial communities of cryoconite holes, small depressions filled with meltwater that form on the surface of Forni Glacier (Italian Alps). Cryoconite holes are considered the most biologically active environments on glaciers. Bacteria can colonize these environments by short-range transport from ice-marginal environments or by long-range transport from distant areas. We used high throughput DNA sequencing to identify Operational Taxonomic Units (OTUs) present in cryoconite holes and three ice-marginal environments, the moraines, the glacier forefield, and a large (> 3 m high) ice-cored dirt cone occurring on the glacier surface. Bacterial communities of cryoconite holes were different from those of ice-marginal environments and hosted fewer OTUs. However, a network analysis revealed that the cryoconite holes shared more OTUs with the moraines and the dirt cone than with the glacier forefield. Ice-marginal environments may therefore act as sources of bacteria for cryoconite holes, but differences in environmental conditions limit the number of bacterial strains that may survive in them. At the same time, cryoconite holes host a few OTUs that were not found in any ice-marginal environment we sampled, thus suggesting that some bacterial populations are positively selected by the specific environmental conditions of the cryoconite holes.

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km2 of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area.

Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. The diversity of alkane hydroxylase (alkB) phylotypes harboured by phyllospheric bacteria associated to urban Platanus trees was also evaluated. Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. On the contrary, diversity of hydrocarbon-degrading populations increased over the months, although it resulted lower than that reported for other habitats. It was therefore hypothesized that atmospheric hydrocarbons might play a key role in the selection of phyllospheric populations in urban areas.

Temporal variability of bacterial communities in cryoconite on an alpine glacier.

Cryoconite holes, that is, small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Bacterial communities in these environments have been extensively studied, but often through snapshot studies based on the assumption of a general stability of community structure. In this study, the temporal variation of bacterial communities in cryoconite holes on the Forni Glacier (Italian Alps) was investigated by high throughput DNA sequencing. A temporal change of bacterial communities was observed with autotrophic Cyanobacteria populations dominating communities after snowmelt, and heterotrophic Sphingobacteriales populations increasing in abundance later in the season. Bacterial communities also varied according to hole depth and area, amount of organic matter in the cryoconite and oxygen concentration. However, variation in environmental features explained a lower fraction of the variation in bacterial communities than temporal variation. Temporal change along ablation season seems therefore more important than local environmental conditions in shaping bacterial communities of cryoconite of the Forni Glacier. These findings challenge the assumption that bacterial communities of cryoconite holes are stable.

Shift in microbial community structure of anaerobic side-stream reactor in response to changes to anaerobic solid retention time and sludge interchange ratio.

A laboratory scale nutrient removal activated sludge system coupled with an anaerobic side-stream reactor was operated for 300 days treating real urban wastewater. A significant decrease in sludge production was obtained increasing the anaerobic solid retention time (SRTASSR) and decreasing the sludge interchange ratio (IR). In this study, the microbial community structure was analyzed and compared with the sludge reduction performance. Quantitative polymerase chain reaction analyses encoding 16 ribosomal RNA and functional genes revealed a wide diversity of phylogenetic groups in each experimental period, resulting from long solids retention time and recirculation of sludge under aerobic, anoxic and anaerobic conditions. However, decreasing SRTASSR from 10 to 2.5d and increasing IR from 27 to 100%, an increasing selection of both fermenting bacteria able to release extracellular polymeric substances and hydrolyze organic matter and slow growing bacteria involved in nutrient removal were detected and linked to the sludge reduction mechanisms.

Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces.

Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers, providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways. Indeed, we observed high abundance of heterotrophic anoxygenic phototrophs, suggesting that light might directly supplement the energy demand of some bacterial strains allowing them to use as carbon source organic molecules, which otherwise would be respired. Furthermore, data suggest that CO2 could be produced also by microbiologically mediated oxidation of CO, which may be produced by photodegradation of organic matter.

Hydrocarbon degrading microbial communities in bench scale aerobic biobarriers for gasoline contaminated groundwater treatment.

BTEX compounds (benzene, toluene, ethylbenzene and xylenes) and methyl tert-butyl ether (MTBE) are some of the main constituents of gasoline and can be accidentally released in the environment. In this work the effect of bioaugmentation on the microbial communities in a bench scale aerobic biobarrier for gasoline contaminated water treatment was studied by 16S rRNA gene sequencing. Catabolic genes (tmoA and xylM) were quantified by qPCR, in order to estimate the biodegradation potential, and the abundance of total bacteria was estimated by the quantification of the number of copies of the 16S rRNA gene. Hydrocarbon concentration was monitored over time and no difference in the removal efficiency for the tested conditions was observed, either with or without the microbial inoculum. In the column without the inoculum the most abundant genera were Acidovorax, Bdellovibrio, Hydrogenophaga, Pseudoxanthomonas and Serpens at the beginning of the column, while at the end of the column Thauera became dominant. In the inoculated test the microbial inoculum, composed by Rhodococcus sp. CE461, Rhodococcus sp. CT451 and Methylibium petroleiphilum LMG 22953, was outcompeted. Quantitative PCR results showed an increasing in xylM copy number, indicating that hydrocarbon degrading bacteria were selected during the treatment, although only a low increase of the total biomass was observed. However, the bioaugmentation did not lead to an increase in the degradative potential of the microbial communities.

Anodic and cathodic microbial communities in single chamber microbial fuel cells.

Microbial fuel cells (MFCs) are a rapidly growing technology for energy production from wastewater and biomasses. In a MFC, a microbial biofilm oxidizes organic matter and transfers electrons from reduced compounds to an anode as the electron acceptor by extracellular electron transfer (EET). The aim of this work was to characterize the microbial communities operating in a Single Chamber Microbial Fuel Cell (SCMFC) fed with acetate and inoculated with a biogas digestate in order to gain more insight into anodic and cathodic EET. Taxonomic characterization of the communities was carried out by Illumina sequencing of a fragment of the 16S rRNA gene. Microorganisms belonging to Geovibrio genus and purple non-sulfur (PNS) bacteria were found to be dominant in the anodic biofilm. The alkaliphilic genus Nitrincola and anaerobic microorganisms belonging to Porphyromonadaceae family were the most abundant bacteria in the cathodic biofilm.

Effect of preservation method on the assessment of bacterial community structure in soil and water samples.

The methods used in sample preservation may affect the description of the microbial community structure by DNA-based techniques. This study aims at evaluating the effect of different storage conditions, including freezing, adding two liquid-based preservatives or simply storing samples with no preservative, on the structure of the microbial communities in aliquots of organic-rich soil and water samples as revealed by a terminal restriction fragment length polymorphisms. The results showed that the number of terminal restriction fragments (TRFs) detected in soil aliquots stored with LifeGuard(™) solution was significantly lower than that of samples analyzed immediately after sampling. Moreover, cluster and PCA analyses showed that soil aliquots stored using LifeGuard(™) clustered separately from those stored with the other methods. Conversely, soil and water aliquots stored with DMSO-EDTA-salt solution did not show either significant reduction in the number of TRFs or any change in the structure of the microbial community. Finally, the number of TRFs and the structure of microbial communities from soil aliquots stored with no preservative did not differ from those of aliquots analyzed immediately after sampling. Preservation methods should therefore be accurately evaluated before collecting samples that have to be stored for long time before DNA extraction.

Unravelling the bacterial diversity in the atmosphere.

The study of airborne biological particles ('bioaerosols') has gained interest in recent years, due to an increasing amount of evidence suggesting that this fraction of airborne particulate matter may play a critical role in the negative effects of aerosols on biological systems. Pioneer investigations demonstrated that bacteria do exist in the atmosphere and can be metabolically active, although studies have not proved whether they actually form ecological communities or are merely assemblages of organisms passively transported from different sources. For a long time, cultivation-based methods have been the gold standard to describe and quantify airborne microorganisms. However, the use of culture-independent techniques and, more recently, of the next-generation sequencing-based methods, has improved the ability of the scientific community to investigate bioaerosols in detail and to address further research questions, such as the temporal and spatial variability of airborne bacterial assemblages, the environmental factors affecting this variability and the potential sources of atmospheric bacteria. This paper provides a systematic review of the state-of-the-art methodologies used in the study of airborne bacteria to achieve each of the aforementioned research objectives, as well as the main results obtained so far. Critical evaluations of the current state of the knowledge and suggestions for further researches are provided.