Microbial growth and resuscitation alter community structure after perturbation

Abstract: An increase in the number of culturable organisms and a decrease in the diversity of recoverable microbiota have been reported in deep subsurface materials after storage perturbation. The magnitude of the microbial community shift in stored samples was more pronounced at 4°C compared to −20°C. Phospholipid fatty acid analyses and acridine orange direct counts indicated that biomass did not increase significantly throughout storage. Changes in the types of fatty acid methyl esters determined over the time course indicated that some of the microbial community shift was due to bacterial proliferation. However, the recovery of new bacterial types only after the storage process suggested that some of the increase in culturable cell count was due to the resuscitation of dormant microorganisms, possibly activated by some aspect of sampling, sample handling, and/or storage. Comparison of acridine orange direct counts with phospholipid and diglyceride fatty acid content suggested that much of the biomass may have been non-living at early time points; however, after 30 days of storage most of the bacterial biomass was viable.     

Amphibian skin may select for rare environmental microbes

Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians'' core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment.     

Pathogens,faecal indicators and human-specific microbial source-tracking markers in sewage

The objective of this review is to assess the current state of knowledge of pathogens, general faecal indicators and human-specific microbial source tracking markers in sewage. Most of the microbes present in sewage are from the microbiota of the human gut, including pathogens. Bacteria and viruses are the most abundant groups of microbes in the human gut microbiota. Most reports on this topic show that raw sewage microbiological profiles reflect the human gut microbiota. Human and animal faeces share many commensal microbes as well as pathogens. Faecal-orally transmitted pathogens constitute a serious public health problem that can be minimized through sanitation. Assessing both the sanitation processes and the contribution of sewage to the faecal contamination of water bodies requires knowledge of the content of pathogens in sewage, microbes indicating general faecal contamination and microbes that are only present in human faecal remains, which are known as the human-specific microbial source-tracking (MST) markers. Detection of pathogens would be the ideal option for managing sanitation and determining the microbiological quality of waters contaminated by sewage; but at present, this is neither practical nor feasible in routine testing. Traditionally, faecal indicator bacteria have been used as surrogate indicators of general faecal residues. However, in many water management circumstances, it becomes necessary to detect both the origin of faecal contamination, for which MST is paramount, and live micro-organisms, for which molecular methods are not suitable. The presence and concentrations of pathogens, general faecal indicators and human-specific MST markers most frequently reported in different areas of the world are summarized in this review.     

Use of the MIDI-FAME technique to characterize groundwater communities

Fatty acid methyl ester (FAME) profiles were identified directly from groundwater microbial communities concentrated on and extracted with polycarbonate filters. The sensitivity of this direct extraction method was determined using pure cultures of Acinetobacter junii, Pseudomonas putida and Stenotrophomonas maltophilia. A minimum concentration of 107 cells filter-1 was required to identify the predominant fatty acids from each culture. However, at least 3.7 x 109 cells filter-1 were required to obtain fatty acid profiles that matched the signature profiles for pure cultures in a commercial database. While several saturated fatty acids (i.e. 14 : 0, 16 : 0, 18 : 0) were extracted from the polycarbonate filters, they were readily subtracted from microbial fatty acid profiles and did not interfere with the characterization of pure cultures or environmental samples. For the environmental samples, 3 l of groundwater from the Savannah River Site, Aiken, SC, (USA) contained sufficient biomass for direct extraction. A comparative analysis of FAME groundwater profiles demonstrated a qualitative difference among communities sampled from spatially discrete locations, while a groundwater well that was sampled at two time points showed strong similarities over time. Concentration of microbial biomass on polycarbonate filters coupled with the MIDI-FAME extraction of both biomass and filter was a useful technique to characterize microbial communities from groundwater.     

Microbial community structure and biomass in developing drinking water biofilms

Traditional techniques to study microbes, such as culturable counts, microbial biomass, or microbial activity, do not give information on the microbial ecology of drinking water systems. The aim of this study was to analyze whether the microbial community structure and biomass differed in biofilms collected from two Finnish drinking water distribution systems (A and B) receiving conventionally treated (coagulation, filtration, disinfection) surface water. Phospholipid fatty acid methyl esters (PLFAs) and lipopolysaccharide 3-hydroxy fatty acid methyl esters (LPS 3-OH-FAs) were analyzed from biofilms as a function of water residence time and development time. The microbial communities were rather stabile through the distribution systems, as water residence time had minor effects on PLFA profiles. In distribution system A, the microbial community structure in biofilms, which had developed in 6 weeks, was more complex than those grown for 23 or 40 weeks. The microbial communities between the studied distribution systems differed, possibly reflecting the differences in raw water, water purification processes, and distribution systems. The viable microbial biomass, estimated on the basis of PLFAs, increased with increasing water residence time in both distribution systems. The quantitative amount of LPS 3-OH-FAs increased with increasing development time of biofilms of distribution system B. In distribution system A, LPS 3-OH-FAs were below the detection limit.     

Effects of Grazing by Estuarine Gammaridean Amphipods on the Microbiota of Allochthonous Detritus

Estuarine gammaridean amphipods grazing at natural population density on detrital microbiota affected the microbial community composition, biomass, and metabolic activity without affecting the physical structure of the leaves. Total microbial biomass estimated by adenosine triphosphate and lipid phosphate or observed by scanning electron microscopy was greater on grazed than on ungrazed detritus. The rates of oxygen consumption, poly-β-hydroxybutyrate synthesis, total lipid biosynthesis, and release of ¹⁴CO₂ from radioactively prelabeled microbiota were higher on grazed than on ungrazed leaves, indicating stimulation of the metabolic activity of grazed detrital microbes. This was true with rates based either on the dry leaf weight or microbial biomass. Alkaline phosphatase activity was lower in the grazed system, consistent with enhanced inorganic phosphate cycling. The loss of ¹⁴C from both total lipid and poly-β-hydroxybutyrate of microorganisms prelabeled with ¹⁴C was greater from grazed than ungrazed microbes. There was a faster decrease in the ¹⁴C-glycolipid than in the ¹⁴C-neutral lipid or ¹⁴C-phospholipid fractions. Analysis of specific phospholipids showed losses of the metabolically stable [¹⁴C]glycerolphosphorylcholine derived from phosphatidylcholine and much more rapid metabolism of the bacterial lipid phosphatidylglycerol measured as [¹⁴C]glycerolphosphorylglycerol with amphipod grazing. The biochemical data supported scanning electron microscopy observations of a shift as the grazing proceeded from a bacterial/fungal community to one dominated by bacteria.     

A Long-Term Field Study of In Situ Bioremediation in a Fractured Conglomerate Trichloroethene Source Zone

ABSTRACT An 8-year bioremediation field study was conducted in a trichloroethene (TCE)-contaminated, highly indurated (i.e., hard), recharge-limited (i.e., contains little water) conglomerate where common remediation strategies, such as groundwater recirculation and direct push installation of a large well network, could not be used. A tracer test using isotopically distinct water from the Hetch Hetchy Reservoir indicated that remediation fluids mainly flowed through fractures and sand lenses in the conglomerate. This was confirmed during in situ bioremediation of the site, in which Dehalococcoides (from a bioaugmentation culture) and volatile fatty acids (from injection of lactate) were the most accurate indicators of transport between wells. Some contaminants were also displaced out of the area due to injection of tracer water. Despite these difficulties, dissolved contaminant mass decreased by an estimated 80% by the end of the test, reaching the lowest values ever recorded at this site. Furthermore, the persistence of ethene 4 years after bioaugmentation suggests that the dechlorinating capacity of the remaining microbial community is comparable to the matrix diffusion of TCE into the dissolved phase.     

Bacterial Communities Associated with Production Facilities of Two Newly Drilled Thermogenic Natural Gas Wells in the Barnett Shale (Texas, USA)

We monitored the bacterial communities in the gas–water separator and water storage tank of two newly drilled natural gas wells in the Barnett Shale in north central Texas, using a 16S rRNA gene pyrosequencing approach over a period of 6?months. Overall, the communities were composed mainly of moderately halophilic and halotolerant members of the phyla Firmicutes and Proteobacteria (classes Βeta-, Gamma-, and Epsilonproteobacteria) in both wells at all sampling times and locations. Many of the observed lineages were encountered in prior investigations of microbial communities from various fossil fluid formations and production facilities. In all of the samples, multiple H₂S-producing lineages were encountered; belonging to the sulfate- and sulfur-reducing class Deltaproteobacteria, order Clostridiales, and phylum Synergistetes, as well as the thiosulfate-reducing order Halanaerobiales. The bacterial communities from the separator and tank samples bore little resemblance to the bacterial communities in the drilling mud and hydraulic-fracture waters that were used to drill these wells, suggesting the in situ development of the unique bacterial communities in such well components was in response to the prevalent geochemical conditions present. Conversely, comparison of the bacterial communities on temporal and spatial scales suggested the establishment of a core microbial community in each sampled location. The results provide the first overview of bacterial dynamics and colonization patterns in newly drilled, thermogenic natural gas wells and highlights patterns of spatial and temporal variability observed in bacterial communities in natural gas production facilities.     

A practical guide for restoration ecologists to manage microbial contamination risks before laboratory processes during microbiota restoration studies

Environmental microbiota are becoming more conventional components of restoration ecology studies due to their functional importance in ecosystems. Studying these microbiota offers insight into how they respond to, and potentially drive, ecosystem restoration. However, microbes are everywhere and therefore they pose a risk to sample integrity via uncontrolled contamination, and many of these risks are introduced before entering a molecular facility. Field ecologists who have limited experience in microbial and/or molecular studies may lack the knowledge on how to mitigate microbial contamination risks and, accordingly, may find rigorous collection of microbial samples a daunting task. Here, we present a practical guide that builds on our previous paper to help manage the risks of microbial contamination when undertaking a microbiota restoration study prior to entering a molecular facility. We cover study design and planning, undertaking field sampling, and sample transport and storage. We hope to provide a useful and practical guide to restoration ecologists who wish to include a microbiota component in their studies. If done well, this inclusion offers improved research quality and ultimately enhanced restoration outcomes.     

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus)

Intestinal microbial communities from 362 anadromous Arctic char (Salvelinus alpinus) from the high Arctic Kitikmeot region, Nunavut, Canada, were characterized using high-throughput 16S rRNA gene sequencing. The resulting bacterial communities were compared across four seasonal habitats that correspond to different stages of annual migration. Arctic char intestinal communities differed by sampling site, salinity and stages of freshwater residence. Although microbiota from fish sampled in brackish water were broadly consistent with taxa seen in other anadromous salmonids, they were enriched with putative psychrophiles, including the nonluminous gut symbiont Photobacterium iliopiscarium that was detected in >90% of intestinal samples from these waters. Microbiota from freshwater-associated fish were less consistent with results reported for other salmonids, and highly variable, possibly reflecting winter fasting behaviour of these char. We identified microbiota links to age for those fish sampled during the autumn upriver migration, but little impact of the intestinal content and water microbiota on the intestinal community. The strongest driver of intestinal community composition was seasonal habitat, and this finding combined with identification of psychrophiles suggested that water temperature and migratory behaviour are key to understanding the relationship between Arctic char and their symbionts.     

Some special problems in the determination of viable counts of groundwater microorganisms

Factors affecting viable cell counts in groundwater or sediments were studied with samples from the Segeberg Forest test area in northern Germany. There was very little variation in results with the season (April, August, November) or depth of sampling; generally there were 10³–10⁴ aerobic cells per ml or g sediment. Long incubation times resulted in higher cell counts; groundwater samples required 4–5 weeks, and sediment extracts had to be cultured for 7 weeks. Total cell counts in sediment were 10²–10⁴ cell/g higher than viable cell counts of aerobes. This was explained partly by the additional presence of anaerobes and partly by the observation that some morphotypes may not have grown under our conditions. Viable cell counts were not influenced by cell extraction from the sediment with either Na-pyrophosphate or groundwater extracts. However, iron-precipitating or manganese-oxidizing bacteria were better extracted with sterile groundwater. The microflora of wells was more numerous than that of the free aquifer; consequently it was better to pump off all well water before aquifer water was sampled. The diameter of the well was also important; thinner tubes had higher cell counts than those with wider diameter. For sampling, wells should be at least 1 year old, since young wells contain higher numbers of microorganisms due to underground disturbances from the drilling. Turbid water samples could be clarified by filtration, but this reduced the viable counts by 1–2 orders of magnitude. Two different media inoculated with a sample dilution resulted in the same cell counts, but their microbial diversity was different. Storage of groundwater samples before processing resulted in up to 17-fold increases in cell counts and loss of diversity in the first 24 hours. Cell numbers decreased slowly during longer storage.     

Biochemical markers for measurement of predation effects on the biomass,community structure,nutritional status,and metabolic activity of microbial biofilms

Chemical measures for the biomass, community structure, nutritional status, and metabolic activities of microbes in biofilms attached to detrital or sediment surfaces based on analysis of components of cells and extracellular polymers represent a quantitative and sensitive method for the analysis of predation. These methods require neither the quantitative removal of the organisms from the surfaces nor the efficient culture of each group of microbes for analysis of predation effects on the biofilm. The biomass of microbes can be determined by measuring the content of cellular components found universally in relatively constant amounts. If these components have a high natural turnover or are rapidly lost from viable cells, they can be utilized to measure the viable cell mass. The membrane phospholipids have a naturally high turnover, are found in all cellular membranes, are rapidly hydrolyzed on cell death, and are found in reasonably constant amounts in bacterial cells as they occur in nature. Estimates of the viable biomass by phospholipid content correspond to estimates from the content of muramic acid, ATP, several enzyme activities, direct cell counts, and in some cases viable counts of subsurface sediments. The analysis of the ester-linked fatty acids of the phospholipids (PLFA) using capillary gas chromatography/mass spectrometry (GC/MS) provides sufficient information for the detection of specific subsets of the microbiota based on patterns of PLFA. With this technique shifts in community structure can be quantitatively assayed. Some of the microbiota form specific components such as poly beta-hydroxyalkanoate (PHA) under conditions of unbalanced growth. Others form polysaccharide glycocalyx when subjected to mechanical or chemical stress. The combination of analysis of phospholipids, PLFA, PHA, and glycocalyx provides a definition of the biomass, community structure, and metabolic status of complex microbial communities. These methods involve chromatographic separation and analysis so rates of incorporation or turnover into specific components can be utilized as measures of metabolic activities. With these methods it has proved possible to show that amphipod grazing can induce shifts in biofilm community structure, nutritional status, and metabolic activities. With this technology it proved possible to show resource partitioning amongst sympatric detrital feeding amphipods, prey specificity of feeding of benthic microvores, effects of sedimentary microtopology on predation, and shifts in the microbiota by exclusion of top epibenthic predators.     

芦苇克隆整合对石油污染湿地土壤微生物群落结构和生物量的影响

克隆植物形体相连的无性个体(分株)之间可以进行水分、养分和光合产物的传递和共享,并且这种克隆整合可以显著提高分株对环境胁迫的耐受能力,从而可能进一步影响分株周围的土壤微生物群落结构和生物量。尽管国内外已经开展了大量有关克隆整合对分株耐受胁迫能力影响的研究,但克隆整合对土壤微生物群落结构和生物量影响的研究却十分缺乏。以黄河三角洲芦苇(Phragmites australis)湿地生态系统为研究对象,将直径60 cm的圆形样方进行三个水平的石油添加处理(不添加石油或每年添加5 mm或10 mm厚的石油),同时通过切断或不切断样方内外芦苇根状茎的连接来控制克隆整合的有无。实验连续开展了两年(2014—2015年),每年8月份在样方内进行土壤样品取样,在实验室内采用磷酸脂肪酸(PLFA)法测定土壤微生物总量及主要微生物类群含量,并测定土壤微生物生物量碳和氮含量。取样时间显著影响土壤微生物PLFA总量、微生物碳和氮含量,这3个变量在2015年均显著高于2014年。石油添加在2015年显著增加了土壤微生物PLFA总量,但在2014年却无显著效应;同时,石油添加在2014年降低了土壤微生物碳和氮含量,而在2015年却增加了其含量。然而,无论在2014年还是2015年,芦苇的克隆整合对土壤微生物PLFA含量、微生物碳和氮含量均没有显著影响。土壤微生物PLFA总量与土壤微生物碳和氮含量呈正相关关系。这些结果表明,石油污染可以显著影响湿地土壤微生物动态,但克隆整合却无显著效应。     

Physiology and microbial community structure in soil at extreme water content

A sandy loam soil was brought to 6 water contents (13-100% WHC) to study the effects of extreme soil moistures on the physiological status of microbiota (represented by biomass characteristics, specific respiration, bacterial growth, and phospholipid fatty acid, PLFA, stress indicators) and microbial community structure (assessed using PLFA fingerprints). In dry soils, microbial biomass and activity declined as a consequence of water and/or nutrient deficiency (indicated by PLFA stress indicators). These microbial communities were dominated by G+ bacteria and actinomycetes. Oxygen deficits in water-saturated soils did not eliminate microbial activity but the enormous accumulation of poly-3-hydroxybutyrate by bacteria showed the unbalanced growth in excess carbon conditions. High soil water content favored G bacteria.     

Molecular Paths Linking Metabolic Diseases,Gut Microbiota Dysbiosis and Enterobacteria Infections

Alterations of both ecology and functions of gut microbiota are conspicuous traits of several inflammatory pathologies, notably metabolic diseases such as obesity and type 2 diabetes. Moreover, the proliferation of enterobacteria, subdominant members of the intestinal microbial ecosystem, has been shown to be favored by Western diet, the strongest inducer of both metabolic diseases and gut microbiota dysbiosis. The inner interdependence between the host and the gut microbiota is based on a plethora of molecular mechanisms by which host and intestinal microbes modify each other. Among these mechanisms are as follows: (i) the well-known metabolic impact of short chain fatty acids, produced by microbial fermentation of complex carbohydrates from plants; (ii) a mutual modulation of miRNAs expression, both on the eukaryotic (host) and prokaryotic (gut microbes) side; (iii) the production by enterobacteria of virulence factors such as the genotoxin colibactin, shown to alter the integrity of host genome and induce a senescence-like phenotype in vitro; (iv) the microbial excretion of outer-membrane vesicles, which, in addition to other functions, may act as a carrier for multiple molecules such as toxins to be delivered to target cells. In this review, I describe the major molecular mechanisms by which gut microbes exert their metabolic impact at a multi-organ level (the gut barrier being in the front line) and support the emerging triad of metabolic diseases, gut microbiota dysbiosis and enterobacteria infections.     

Analysis of Lung Microbiota in Bronchoalveolar Lavage,Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease

Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV₁>50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease.     

Comparison of microbial community compositions of injection and production well samples in a long-term water-flooded petroleum reservoir

Water flooding plays an important role in recovering oil from depleted petroleum reservoirs. Exactly how the microbial communities of production wells are affected by microorganisms introduced with injected water has previously not been adequately studied. Using denaturing gradient gel electrophoresis (DGGE) approach and 16S rRNA gene clone library analysis, the comparison of microbial communities is carried out between one injection water and two production waters collected from a working block of the water-flooded Gudao petroleum reservoir located in the Yellow River Delta. DGGE fingerprints showed that the similarities of the bacterial communities between the injection water and production waters were lower than between the two production waters. It was also observed that the archaeal composition among these three samples showed no significant difference. Analysis of the 16S rRNA gene clone libraries showed that the dominant groups within the injection water were Betaproteobacteria, Gammaproteobacteria and Methanomicrobia, while the dominant groups in the production waters were Gammaproteobacteria and Methanobacteria. Only 2 out of 54 bacterial operational taxonomic units (OTUs) and 5 out of 17 archaeal OTUs in the injection water were detected in the production waters, indicating that most of the microorganisms introduced by the injection water may not survive to be detected in the production waters. Additionally, there were 55.6% and 82.6% unique OTUs in the two production waters respectively, suggesting that each production well has its specific microbial composition, despite both wells being flooded with the same injection water.     

Lipid analysis of the response of a sedimentary microbial community to polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAH) are widespread environmental contaminants that can, under proper conditions, be degraded by microorganisms. The responses of a riverine sedimentary microbial community to PAH contamination were examined using an integrated biochemical assay that yielded data on PAH concentration, total microbial biomass, and microbial community structure and were interpreted using perturbation theory and the subsidy-stress gradient. Microbial mineralization of naphthalene, anthracene, fluorene, and phenanthrene was observed 24 h after their addition to all sediments sampled and ranged from 0.9 to 16.3% in ambient sediments and from 14.8 to 35.8% in contaminated sediments. Total microbial biomass, determined by phospholipid phosphate, increased in response to intermediate PAH concentration and decreased at sites with the highest PAH concentration (p < 0.05) during seven out of nine (78%) seasonal sampling periods. The two sampling periods that were not statistically different followed periods of high water and cold temperatures. Phospholipid fatty acid analysis of microbial community structure analysis indicated that increases in the relative abundance of gram-negative aerobes and heterotrophic eukaryotes were responsible, in part, for these observed increases in total microbial biomass. These findings (increased degradation rates, increased biomass at intermediate PAH concentrations, and altered community structure) indicate that a component of the microbial community responded to PAH as a usable input and are consistent with the predictions of perturbation theory and a subsidy-stress gradient.     

The Dynamic Distribution of Porcine Microbiota across Different Ages and Gastrointestinal Tract Segments

Metagenome of gut microbes has been implicated in metabolism, immunity, and health maintenance of its host. However, in most of previous studies, the microbiota was sampled from feces instead of gastrointestinal (GI) tract. In this study, we compared the microbial populations from feces at four different developmental stages and contents of four intestinal segments at maturity to examine the dynamic shift of microbiota in pigs and investigated whether adult porcine fecal samples could be used to represent samples of the GI tract. Analysis results revealed that the ratio of Firmicutes to Bacteroidetes from the feces of the older pigs (2-, 3-, 6- month) were 10 times higher compared to those from piglets (1-month). As the pigs matured, so did it seem that the composition of microbiome became more stable in feces. In adult pigs, there were significant differences in microbial profiles between the contents of the small intestine and large intestine. The dominant genera in the small intestine belonged to aerobe or facultative anaerobe categories, whereas the main genera in the large intestine were all anaerobes. Compared to the GI tract, the composition of microbiome was quite different in feces. The microbial profile in large intestine was more similar to feces than those in the small intestine, with the similarity of 0.75 and 0.38 on average, respectively. Microbial functions, predicted by metagenome profiles, showed the enrichment associated with metabolism pathway and metabolic disease in large intestine and feces while higher abundance of infectious disease, immune function disease, and cancer in small intestine. Fecal microbes also showed enriched function in metabolic pathways compared to microbes from pooled gut contents. Our study extended the understanding of dynamic shift of gut microbes during pig growth and also characterized the profiles of bacterial communities across GI tracts of mature pigs.     

Responses of soil microorganisms to resource availability in urban, desert soils

Terrestrial desert ecosystems are strongly structured by the distribution of plants, which concentrate resources and create islands of fertility relative to interplant spaces. Atmospheric nitrogen (N) deposition resulting from urbanization has the potential to change those spatial patterns via resource inputs, resulting in more homogeneous soil resource availability. We sampled soils at 12 desert remnant sites around Phoenix, Arizona along a model-predicted gradient in N deposition to determine the degree to which deposition has altered spatial patterns in soil resource availability and microbial activity. Soil microbial biomass and abundance were not influenced by atmospheric N deposition. Instead, plant islands remained strong organizers of soil microbial processes. These islands of fertility exhibited elevated pools of resources, microbial abundance, and activity relative to interspaces. In both plant islands and interspaces, soil moisture and soil N concentrations predicted microbial biomass and abundance. Following experimental wetting, carbon dioxide (CO₂) flux from soil of interspaces was positively correlated with N deposition, whereas in plant islands, soil CO₂ flux was positively correlated with soil moisture content and soil organic matter. Soil CO₂ flux in both patch types showed rapid and short-lived responses to precipitation, demonstrating the brief time scales during which soil biota may process deposited materials. Although we observed patterns consistent with N limitation of microbes in interspaces, we conclude that atmospheric N deposition likely accumulates in soils because microbes are primarily limited by water and secondarily by carbon or nitrogen. Soil microbial uptake of atmospherically deposited N likely occurs only during sparse and infrequent rainfall.