Spatial Distribution Of Bacteria Research Articles

Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods

The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.

Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea

Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.

Advances and Challenges in Fluorescence in situ Hybridization for Visualizing Fungal Endobacteria.

Several bacteria have long been known to interact intimately with fungi, but molecular approaches have only recently uncovered how cosmopolitan these interactions are in nature. Currently, bacterial–fungal interactions (BFI) are inferred based on patterns of co-occurrence in amplicon sequencing investigations. However, determining the nature of these interactions, whether the bacteria are internally or externally associated, remains a grand challenge in BFI research. Fluorescence in situ hybridization (FISH) is a robust method that targets unique sequences of interest which can be employed for visualizing intra-hyphal targets, such as mitochondrial organelles or, as in this study, bacteria. We evaluate the challenges and employable strategies to resolve intra-hyphal BFI to address pertinent criteria in BFI research, such as culturing media, spatial distribution of bacteria, and abundance of bacterial 16S rRNA copies for fluorescent labeling. While these experimental factors influence labeling and detection of endobacteria, we demonstrate how to overcome these challenges thorough permeabilization, appropriate media choice, and targeted amplification using hybridization chain reaction FISH. Such microscopy imaging approaches can now be utilized by the broader research community to complement sequence-based investigations and provide more conclusive evidence on the nature of specific bacterial–fungal relationships.

БАКТЕРИОБЕНТОС НАИЛКА В ПРИПЛОТИННОМ ПЛЕСЕ КУЙБЫШЕВСКОГОВОДОХРАНИЛИЩА

For the first time, the distribution of the total number and biomass of bacteria, the number of saprophytic bacteria and the size-morphological structure of bacteriobenthos in the suspended sediment of the Priplotinny Reach of the Kuibyshev reservoir were studied. The surface layer of the watered sediment (0.5-1 cm) was studied. The average number of bacteria in the suspended sediment is estimated at 5.19±1.52×109cells mL-1, biomass – 0.68±0.25 μg mL-1. The average number of saprophytic bacteria is 5.82±0.53×105 CFUmL-1. The size structure is dominated by bacterial cells with linear dimensions of 0.2-0.5 μmand a volume of 0.025-0.100 µm3.The dominant cellmorphotypeis rods.The percentage of coccobacilli is higher in the littoral, rods – in the profundal. A comparative analysis of bacteriobenthos in the suspended and in the bottom sediments (1-2 cm) was carried out. In the vertical profile,towards the bottom the total number and biomass of bacteria increases, the variability of the dominant size classes of bacteria increases, and by an order of magnitude the percentage of saprophytic bacteria decreases. Spatial distribution of bacteria in suspended sediment conserves the general pattern common for silts– an increase in the number and biomass of cells from upper reaches towards the dam. The exception is the headwater sectionwith increased hydrodynamic activity of bottom waters resulting in decreased quantities of bacteria in the suspended sediment compared to bottom sediment. The largest numbers of saprophytic bacteria on the shallow coast are concentrated in the bottom sediment, in the deep–water central zone of the reach – in the suspended sediment. The distribution of cocci in the upper sediment along the bottom is uniform and does not change with depth. In the bottom sediment cocci reach their greatest quantities in shallow waters, in deep-water biotopes their number decreases.

Presence and abundance of bacteria with the Type VI secretion system in a coastal environment and in the global oceans.

Marine bacteria employ various strategies to maintain their competitive advantage over others in a mixed community. The use of Type VI Secretion Systems (T6SS), a protein secretion apparatus used as a molecular weapon for interbacterial competition and eukaryotic interactions, is one of the competitive strategies that is least studied among heterotrophic bacteria living in the water column. To get an insight into the temporal and spatial distribution of bacteria with T6SS in this portion of the marine environment, we examine the presence and abundance of T6SS-bearing bacteria at both local and global scales through the use of metagenome data from water samples obtained from the coast of Monterey Bay and the TARA Oceans project. We also track the abundance of T6SS-harboring bacteria through a two-year time series of weekly water samples in the same coastal site to examine the environmental factors that may drive their presence and abundance. Among the twenty-one T6SS-bearing bacterial genera examined, we found several genera assume a particle-attached lifestyle, with only a few genera having a free-living lifestyle. The abundance of T6SS-harboring bacteria in both niches negatively correlates with the abundance of autotrophs. Globally, we found that T6SS genes are much more abundant in areas with low biological productivity. Our data suggest that T6SS-harboring bacteria tend to be abundant spatially and temporally when organic resources are limited. This ecological study agrees with the patterns observed from several in vitro studies; that T6SS could be an adaptive strategy employed by heterotrophic bacteria to obtain nutrients or reduce competition when resources are in limited quantity.

Influence of interspecies interactions on the spatial organization of dual species bacterial communities

Interspecies interactions in bacterial biofilms have important impacts on the composition and function of communities in natural and engineered systems. To investigate these interactions, synthetic communities provide experimentally tractable systems. Biofilms grown on agar-surfaces have been used for investigating the eco-evolutionary and biophysical forces that determine community composition and spatial distribution of bacteria. Prior studies have used genetically identical bacterial strains and strains with specific mutations, that express different fluorescent proteins, to investigate intraspecies interactions. Here, we investigated interspecies interactions and, specifically, determined the community composition and spatial distribution in synthetic communities of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae. Using quantitative microscopic imaging, we found that interspecies interactions in multispecies colonies were influenced by type IV pilus mediated motility, extracellular matrix secretion, environmental parameters, and these effects were also influenced by the specific partner in the dual species combinations. These results indicate that the patterns observable in mixed species colonies can be used to understand the mechanisms that drive interspecies interactions, which are dependent on the interplay between specific species’ physiology and environmental conditions.

Litterbox-A gnotobiotic Zeolite-Clay System to Investigate Arabidopsis-Microbe Interactions.

Plants are colonised by millions of microorganisms representing thousands of species with varying effects on plant growth and health. The microbial communities found on plants are compositionally consistent and their overall positive effect on the plant is well known. However, the effects of individual microbiota members on plant hosts and vice versa, as well as the underlying mechanisms, remain largely unknown. Here, we describe “Litterbox”, a highly controlled system to investigate plant–microbe interactions. Plants were grown gnotobiotically, otherwise sterile, on zeolite-clay, a soil replacement that retains enough moisture to avoid subsequent watering. Litterbox-grown plants resemble greenhouse-grown plants more closely than agar-grown plants and exhibit lower leaf epiphyte densities (106 cfu/g), reflecting natural conditions. A polydimethylsiloxane (PDMS) sheet was used to cover the zeolite, significantly lowering the bacterial load in the zeolite and rhizosphere. This reduced the likelihood of potential systemic responses in leaves induced by microbial rhizosphere colonisation. We present results of example experiments studying the transcriptional responses of leaves to defined microbiota members and the spatial distribution of bacteria on leaves. We anticipate that this versatile and affordable plant growth system will promote microbiota research and help in elucidating plant-microbe interactions and their underlying mechanisms.

Eubacterial fluorescence in situ hybridisation and histologic features in 25 dogs with gallbladder mucocele.

To detect and localise bacteria in gallbladder mucoceles using fluorescence in situ hybridisation (FISH). To report clinical signs, clinicopathologic abnormalities, sonographic findings and histopathological findings in FISH+ and FISH- dogs with gallbladder mucoceles. Retrospective review of signalment, clinical signs, clinicopathologic and sonographic findings of 25 cases of histopathologically confirmed gallbladder mucocele. Histopathological sections of gallbladder mucocele were evaluated for cystic mucinous hyperplasia, cystic mucinous hyperplasia with cholecystitis and rupture. The number and spatial distribution of bacteria was determined by eubacterial FISH. Gallbladder contents were cultured in 21 dogs. Bacteria were detected within or adherent to the gallbladder wall in eight of 25 (32%) cases. Bacterial culture was positive in one dog. Cystic mucinous hyperplasia with concurrent cholecystitis was found in 17 of 25 (68%) of dogs with gallbladder mucocele. FISH was more sensitive for detection of bacteria in gallbladder mucoceles when compared to bacterial culture of bile. Cholecystitis was common in dogs with gallbladder mucocele. Further study is required to elucidate the relationship of cystic mucinous hyperplasia, bacteria and cholecystitis in the aetiopathogenesis and progression of gallbladder mucocele.

Bacterioneuston in Lake Baikal: Abundance, Spatial and Temporal Distribution.

An aquatic surface microlayer covers more than 70% of the world’s surface. Our knowledge about the biology of the surface microlayer of Lake Baikal, the most ancient lake on Earth with a surface area of 31,500 km2, is still scarce. The total bacterial abundance, the number of cultured heterotrophic temporal bacteria, and the spatial distribution of bacteria in the surface microlayer and underlying waters of Lake Baikal were studied. For the first time, the chemical composition of the surface microlayer of Lake Baikal was determined. There were significant differences and a direct relationship between the total bacterial abundance in the surface microlayer and underlying waters of Lake Baikal, as well as between the number of cultured heterotrophic bacteria in studied water layers in the period of summer stratification. In the surface microlayer, the share of cultured heterotrophic bacteria was higher than in the underlying waters. The surface microlayer was characterized by enrichment with PO43−, total organic carbon and suspended particulate matter compared to underlying waters. A direct relationship was found between the number of bacteria in the surface microlayer and environmental factors, including temperature, total organic carbon and suspended particulate matter concentration.

Microbiological studies of Lake Baikal in a Limnological institute: past and present

The article deals with the history of studies of microbial communities in Lake Baikal performed by the researchers of Limnological Institute SB RAS. We provide the information about the studies of freshwater organisms in the world and the formation of aquatic microbiology in Russia. Initial data on bacteria from the lake were obtained in the 1920s of the past century. The studies were carried out at Baikal Biological Station and Baikal Limnological Station of the USSR Academy of Sciences. The frst studies and large discoveries at Lake Baikal were made by microbiologists who came at different times from research institutes of Moscow and Leningrad. When Baikal Limnological Station was reorganized into Limnological Institute of the USSR Academy of Sciences, the studies of microorganisms in Lake Baikal became systematic and complex, and they were mostly performed by the researchers from the Laboratory of Aquatic Microbiology. The long-term regular observations have provided signifcant results on the species composition, abundance, seasonal and interannual dynamics, horizontal and spatial distribution of bacteria in the water column and bottom sediments of Lake Baikal, as well as their functional role. In the past decades, the introduction of molecular-biological, electronic-microscopic and analytical methods allowed determination of the genetic, taxonomic and morphological diversity of bacteria and viruses. Since 2009, main research area of Laboratory of Aquatic Microbiology is the study of bioflm microbiocenoses, including the determination of the taxonomic composition, structural organization, formation features, as well as biotechnological potential of bacterial and viral communities of the surface microlayer of water and bioflms formed on biogenic and abiogenic substrates. The 90-year period of microbiological research of a unique ecosystem of Lake Baikal appeared to besuccessful and rich in discoveries.

Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields

The spatial distribution of bacteria in bulk soil has been well studied, but little is known about the bacterial biogeography in the rhizosphere of crops. Here, we investigated bacterial distribution in bulk soil, loosely- and tightly-bound soils, from wheat fields distributed across 800,000 km2 of the North China Plain. Bacterial community composition differed dramatically among bulk and rhizospheric soils, and bacterial diversity decreased with the root proximity. Soil pH correlated with bacterial community composition and diversity in three compartments. Bacterial community in tightly bound soil formed a hub-based network topology with higher transitivity and greater number of central nodes compared with loosely bound and bulk soils, potentially as a result of more direct ecological interactions between the members of the tightly bound soil compartment. Bulk and rhizospheric soils maintained similar compositional distance decay patterns (with equal decay rates), but distinct phylogenetic distance decay patterns (with steeper slope of tightly bound soil). Geographical distance described a relatively greater proportion of bacterial spatial distribution in tightly bound soil, compared with loosely bound soil and bulk soil. Deterministic processes dominated the assemblage of bacterial communities in all soil compartments, while phylogenetic clustering was weaker in tightly bound soil. Taken together, our results suggest distinct bacterial network structure and distribution patterns among bulk soil, loosely bound soil and tightly bound rhizospheric soil, which could possibly result in potential functional differentiation.

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.

Identification of Mucosa-Invading and Intravascular Bacteria in Feline Small Intestinal Lymphoma

Persistent bacterial infections of the gastrointestinal mucosa are causally linked to gastric carcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma in people and laboratory animals. We examined the relationship of mucosa-associated bacteria to alimentary lymphoma in cats. Intestinal biopsies from 50 cats with alimentary lymphoma (small cell, n = 33; large cell, n = 17) and 38 controls without lymphoma (normal to minimal change on histopathology, n = 18; lymphocytic-plasmacytic enteritis, n = 20) were evaluated. The number and spatial distribution of bacteria (ie, in luminal cellular debris, villus-associated mucus, adherent to epithelium, mucosal invasion, intravascular, or serosal) were determined by fluorescence in situ hybridization with the eubacterial probe EUB-338. Mucosa-invasive bacteria were more frequently observed in cats with large cell lymphoma (82%, P ≤ .001) than in cats with small cell lymphoma (18%), normal to minimal change on histopathology, and lymphocytic-plasmacytic enteritis (3%). Intravascular bacteria were observed solely in large cell lymphoma (29%), and serosal colonization was more common in cats with large cell lymphoma (57%) than with small cell lymphoma (11%, P ≤ .01), normal to minimal change (8%, P ≤ .01), and lymphocytic-plasmacytic enteritis (6%, P ≤ .001). The high frequency of invasive bacteria within blood vessels and serosa of cats with large cell lymphoma may account for the sepsis-related complications associated with large cell lymphoma and inform clinical management. Further studies are required to determine the role of intramucosal bacteria in the etiopathogenesis of feline alimentary lymphoma.

Bacterial Community Structure at the Microscale in Two Different Soils.

The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5cm, whereas the core taxa were distributed in a distance range less than 3mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean

Besides being critical components of marine food web, microorganisms play vital roles in biogeochemical cycling of nutrients and elements in the ocean. Currently little is known about microbial population structure and their distributions in the eastern Indian Ocean. In this study, we applied molecular approaches including polymerase chain reaction-denaturant gradient gel electrophoresis (PCR-DGGE) and High-Throughput next generation sequencing to investigate bacterial 16S rRNA genes from the equatorial regions and the adjacent Bay of Bengal in the eastern Indian Ocean. In general, Bacteroidetes, Proteobacteria (mainly Alpha, and Gamma), Actinobacteria, Cyanobacteria and Planctomycetes dominated the microbial communities. Horizontally distinct spatial distribution of major microbial groups was observed from PCR-DGGE gel image analyses. However, further detailed characterization of community structures by pyrosequencing suggested a more pronounced stratified distribution pattern: Cyanobacteria and Actinobacteria were more predominant at surface water (25 m); Bacteroidetes dominated at 25 m and 150 m while Proteobacteria (mainly Alphaproteobacteria) occurred more frequently at 75 m water depth. With increasing water depth, the bacterial communities from different locations tended to share high similarity, indicating a niche partitioning for minor groups of bacteria recovered with high throughput sequencing approaches. This study provided the first “snapshot” on biodiversity and spatial distribution of Bacteria in water columns in the eastern Indian Ocean, and the findings further emphasized the potential functional roles of these microbes in energy and resource cycling in the eastern Indian Ocean.

State of heterotrophic bacterioplankton of Yenisei estuary and the zone of Ob–Yenisei discharge in autumn in relation with environmental factors

In September 2011, variations of the total abundance of bacteria were studied, including, for the first time, the abundance of bacteria with intact membranes and active electron transport chains, as well as chlorophyll a concentrations and some hydrological and hydrochemical characteristics of water in Yenisei estuary and the zone of Ob–Yenisei river discharge. The study found abundant, viable, and actively functioning bacterioplankton to exist in the region. The absolute values of all microbiological characteristics were found to decrease with the distance from the freshened waters of Yenisei estuary toward the seawater of the Ob–Yenisei river discharge, while the percentage of bacteria with intact membranes and actively functioning microorganisms in bacterioplankton increased in the same direction. Positive correlations were found to exist between the values of all examined microbiological characteristics and the concentration in water of chlorophyll a, silicium, organic nitrogen, and oxygen, as well as water temperature. The same biological characteristics showed negative correlations with water salinity and phosphates. The spatial distribution of bacteria in the examined water body was supposed to be due mostly to the intensity of hydrodynamic processes, rather than the biogenic matter content of water.

Flagella, flexibility and flow: Physical processes in microbial ecology

How microorganisms interact with their environment and with their conspecifics depends strongly on their mechanical properties, on the hydrodynamic signatures they generate while swimming and on fluid flows in their environment. The rich fluid-structure interaction between flagella – the appendages microorganisms use for propulsion – and the surrounding flow, has broad reaching effects for both eukaryotic and prokaryotic microorganisms. Here, we discuss selected recent advances in our understanding of the physical ecology of microorganisms, which have hinged on the ability to directly interrogate the movement of individual cells and their swimming appendages, in precisely controlled fluid environments, and to image them at appropriately fast timescales. We review how a flagellar buckling instability can unexpectedly serve a fundamental function in the motility of bacteria, we elucidate the role of hydrodynamics and flexibility in the emergent properties of groups of eukaryotic flagella, and we show how fluid flows characteristic of microbial habitats can strongly bias the migration and spatial distribution of bacteria. The topics covered here are illustrative of the potential inherent in the adoption of experimental methods and conceptual frameworks from physics in understanding the lives of microorganisms.

Source identification of nitrous oxide on autotrophic partial nitrification in a granular sludge reactor

Emission of nitrous oxide (N2O) during biological wastewater treatment is of growing concern since N2O is a major stratospheric ozone-depleting substance and an important greenhouse gas. The emission of N2O from a lab-scale granular sequencing batch reactor (SBR) for partial nitrification (PN) treating synthetic wastewater without organic carbon was therefore determined in this study, because PN process is known to produce more N2O than conventional nitrification processes. The average N2O emission rate from the SBR was 0.32 ± 0.17 mg-N L−1 h−1, corresponding to the average emission of N2O of 0.8 ± 0.4% of the incoming nitrogen load (1.5 ± 0.8% of the converted NH4+). Analysis of dynamic concentration profiles during one cycle of the SBR operation demonstrated that N2O concentration in off-gas was the highest just after starting aeration whereas N2O concentration in effluent was gradually increased in the initial 40 min of the aeration period and was decreased thereafter. Isotopomer analysis was conducted to identify the main N2O production pathway in the reactor during one cycle. The hydroxylamine (NH2OH) oxidation pathway accounted for 65% of the total N2O production in the initial phase during one cycle, whereas contribution of the NO2− reduction pathway to N2O production was comparable with that of the NH2OH oxidation pathway in the latter phase. In addition, spatial distributions of bacteria and their activities in single microbial granules taken from the reactor were determined with microsensors and by in situ hybridization. Partial nitrification occurred mainly in the oxic surface layer of the granules and ammonia-oxidizing bacteria were abundant in this layer. N2O production was also found mainly in the oxic surface layer. Based on these results, although N2O was produced mainly via NH2OH oxidation pathway in the autotrophic partial nitrification reactor, N2O production mechanisms were complex and could involve multiple N2O production pathways.

Stratification of bacterial concentrations, from upper to lower, in broiler litter

There have been numerous research studies concerning the different types of bacteria in broiler litter. However, very little is known about the spatial distribution of bacteria from the top to the bottom of the litter bed. Two experiments were conducted, one of a single flock in a pen trial, and the second on a commercial broiler farm for 8 consecutive flocks. Core litter samples were taken and 3 fractions of litter were removed from each core for bacterial analysis: the upper 5.08 cm of litter, the exact middle of the litter, and the lower section of litter directly on top of the dirt pad, being sure to include some dirt pad. Core litter samples were taken specifically at 7 d before placement then again at 1, 7, 14, 21, 35, and 49 d of age in experiment 1, and 14 and 35 d of age in experiment 2. Core samples were removed from 6 pens in the first experiment. In experiment 2, core litter samples were taken near the evaporative cooling cells, the environmental control room or middle of the house, and near the exhaust fans. Litter fractions were analyzed for Staphylococcus spp., Clostridium perfringens, Escherichia coli, Salmonella spp., total aerobes, and total anaerobes. A decrease was observed from the top to middle and from middle to bottom fractions of litter for all bacteria. From upper to lower, all bacteria concentrations were reduced by at least 99%. Therefore, the concentration of bacterial populations within broiler litter could shift dramatically within only a few inches of litter and the lower fraction of litter holds relatively less bacteria than the upper or middle fractions.

Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are among the most extreme habitats on Earth, where microbial life exists.