Bacterial Population Structure of the Jute-Retting Environment

Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality.     

The Effects of a Probiotic Yeast on the Bacterial Diversity and Population Structure in the Rumen of Cattle

It has been suggested that the ability of live yeast to improve milk yield and weight gain in cattle is because the yeast stimulates bacterial activity within the rumen. However it remains unclear if this is a general stimulation of all species or a specific stimulation of certain species. Here we characterised the change in the bacterial population within the rumen of cattle fed supplemental live yeast. Three cannulated lactating cows received a daily ration (24 kg/d) of corn silage (61% of DM), concentrates (30% of DM), dehydrated alfalfa (9% of DM) and a minerals and vitamins mix (1% of DM). The effect of yeast (BIOSAF SC 47, Lesaffre Feed Additives, France; 0.5 or 5 g/d) was compared to a control (no additive) in a 3×3 Latin square design. The variation in the rumen bacterial community between treatments was assessed using Serial Analysis of V1 Ribosomal Sequence Tag (SARST-V1) and 454 pyrosequencing based on analysis of the 16S rRNA gene. Compared to the control diet supplementation of probiotic yeast maintained a healthy fermentation in the rumen of lactating cattle (higher VFA concentration [high yeast dose only], higher rumen pH, and lower Eh and lactate). These improvements were accompanied with a shift in the main fibrolytic group (Fibrobacter and Ruminococcus) and lactate utilising bacteria (Megasphaera and Selenomonas). In addition we have shown that the analysis of short V1 region of 16s rRNA gene (50–60 bp) could give as much phylogenetic information as a longer read (454 pyrosequencing of 250 bp). This study also highlights the difficulty of drawing conclusions on composition and diversity of complex microbiota because of the variation caused by the use of different methods (sequencing technology and/or analysis).     

Genetic Population Structure of the Soil Bacterium Myxococcus xanthus at the Centimeter Scale

Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.     

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R² = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.The biogeographical patterns exhibited by microbial communities have been examined in a wide range of environments, and studies focusing on microbial biogeography continue to be published at a rapid pace. We know that microbial community diversity and composition can vary considerably across space, and this variation is theorized to be linked to changes in a number of biotic or abiotic factors (22, 36, 41). There are numerous overarching reasons for this interest in understanding microbial biogeography. For example, comparing microbial patterns to those commonly observed in plant and animal taxa is of intense theoretical interest (22, 25). From a more practical standpoint, studies of microbial biogeography can often provide key insights into the physiologies, environmental tolerances, and ecological strategies of microbial taxa, particularly those difficult-to-culture taxa that often dominate in natural environments. However, perhaps the most important rationale for studying microbial biogeography is the most basic one: microbes are diverse, ubiquitous, and abundant, yet their biogeographical patterns and the factors driving these spatial patterns often remain poorly understood.No single biogeographical pattern is shared by all microorganisms, just as there is no single biogeographical pattern followed by all “macrobial” (i.e., plant and animal) communities (31). The specific biogeographical patterns exhibited by microorganisms are variable and highly dependent on a number of factors, including the taxonomic group in question (29), the degree of phylogenetic resolution at which the communities are examined (e.g., Pseudomonas) (7), and the spatial scale of the study (40). However, some common patterns emerge if we specifically examine the biogeography of soil microorganisms. In particular, the structure and diversity of soil bacterial communities have been found to be closely related to soil environmental characteristics (5, 37, 47), and soil pH is often correlated with the observed biogeographical patterns (19, 24). However, due to the paucity of detailed and comprehensive studies of soil bacterial biogeography, particularly across larger spatial scales, our understanding of soil microbial biogeography remains incomplete.Previous studies of soil bacterial biogeography have focused on either surveying a few soils in detail or surveying a larger number of soils by techniques that offer less detailed phylogenetic information. For example, a few recent studies used pyrosequencing or Sanger sequencing-based techniques to deeply survey the diversity and composition of the bacterial communities within a single soil or a few soils (1, 14, 20, 39, 42). Such studies are valuable in that they provide our best assessments of overall bacterial diversity and community structure and the relative abundances of specific bacterial taxa within soils. However, because such studies often examine only a limited number of soils, they do not allow for robust assessment of biogeographical patterns and the factors that may drive these patterns. Other studies have examined bacterial communities across a larger number of soils, using more limited techniques, such as fingerprinting methods that offer little specific phylogenetic information on bacterial community structure or techniques that describe communities at very coarse levels of taxonomic resolution (18, 19). A comprehensive assessment of the biogeographical patterns exhibited by soil bacterial communities requires both depth (individual communities surveyed at a reasonable level of phylogenetic detail) and breadth (examining a sufficiently large number of samples to assess spatial patterns). With the recent development of the bar-coded pyrosequencing technique (23), we need not sacrifice depth for breadth, or vice versa. This was demonstrated in several recent studies (2, 12, 17, 28) that used bar-coded pyrosequencing to simultaneously analyze relatively large numbers of individual samples, surveying the bacterial community in each sample to an extent that would be difficult (or prohibitively expensive) using standard cloning and Sanger sequencing techniques.Here we apply the bar-coded pyrosequencing technique to examine the structure and diversity of bacterial communities in 88 soils collected from across North and South America. This work expands on a previous fingerprinting-based survey of bacterial communities across a similar set of soils (19), using the pyrosequencing technique to extend the analyses and to answer the following questions. Which taxa are most abundant in soil? How does the phylogenetic structure of bacterial communities vary across the continental scale? Which environmental factors best predict bacterial community structure and diversity? Are some soil bacterial phyla more diverse than others?     

Effects of Culturing on the Population Structure of a Hyperthermophilic Virus

The existence of a culturing bias has long been known when sampling organisms from the environment. This bias underestimates microbial diversity and does not accurately reflect the most ecologically relevant species. Until now no study has examined the effects of culture bias on viral populations. We have employed culture-independent methods to assess the diversity of Sulfolobus spindle–shaped viruses (SSVs) from extremely hyperthermal environments. This diversity is then compared to the viral diversity of cultured samples. We detected a clear culturing bias between environmental samples and cultured isolates. This is the first study identifying a culture bias in a viral population.     

Direct and Indirect Effects of Protist Predation on Population Size Structure of a Bacterial Strain with High Phenotypic Plasticity

We studied the impact of grazing and substrate supply on the size structure of a freshwater bacterial strain (Flectobacillus sp.) which showed pronounced morphological plasticity. The cell length varied from 2 to >40 μm and encompassed rods, curved cells, and long filaments. Without grazers and with a sufficient substrate supply, bacteria grew mainly in the form of medium-sized rods (4 to 7 μm), with a smaller proportion (<10%) of filamentous forms. Grazing experiments with the bacterivorous flagellate Ochromonas sp. showed that freely suspended cells of <7 μm were highly vulnerable to grazers, whereas filamentous cells were resistant to grazing and became enriched during predation. A comparison of long-term growth in carbon-limited chemostats with and without grazers revealed that strikingly different bacterial populations developed: treatments with flagellates were composed of >80% filamentous cells. These attained a biomass comparable to that of populations in chemostats without grazers, which were composed of medium-sized rods and c-shaped cells. Carbon starvation resulted in a fast decrease in cell length and a shift towards small rods, which were highly vulnerable to grazing. Dialysis bag experiments in combination with continuous cultivation revealed that filament formation was significantly enhanced even without direct contact of bacteria with bacterivores and was thus probably stimulated by grazer excretory products.     

Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species F_IT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.     

Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses

Lipopolysaccharides (LPS) are a main constituent of the outer membrane of Gram-negative bacteria. Salmonella enterica, like many other bacterial species, are able to chemically modify the structure of their LPS molecules through the PhoPQ pathway as a defense mechanism against the host immune response. These modifications make the outer membrane more resistant to antimicrobial peptides (AMPs), large lipophilic drugs, and cation depletion, and are crucial for survival within a host organism. It is believed that these LPS modifications prevent the penetration of large molecules and AMPs through a strengthening of lateral interactions between neighboring LPS molecules. Here, we performed a series of long-timescale molecular dynamics simulations to study how each of three key S. enterica lipid A modifications affect bilayer properties, with a focus on membrane structural characteristics, lateral interactions, and the divalent cation bridging network. Our results discern the unique impact each modification has on strengthening the bacterial outer membrane through effects such as increased hydrogen bonding and tighter lipid packing. Additionally, one of the modifications studied shifts Ca²⁺ from the lipid A region, replacing it as a major cross-linking agent between adjacent lipids and potentially making bacteria less susceptible to AMPs that competitively displace cations from the membrane surface. These results further improve our understanding of outer membrane chemical properties and help elucidate how outer membrane modification systems, such as PhoPQ in S. enterica, are able to alter bacterial virulence.     

Population Size and Selection Intensity Effects on Long-Term Selection Response in Mice

Long-term response to within full-sib family selection for increased postweaning gain was evaluated in lines having different effective population sizes (N_e) and selection intensities (i). Line designations were I4(4), I8(2), I16(2), M4(4), M8(2) and M16(2), where I and M indicate selection of the top 50% and 25%, respectively; 4, 8 and 16 represent the number of parental pairs per replicate and number of replicates is given in parentheses. Realized within full-sib family heritabilities (h_R²) in the first phase of selection (0-14 generations) were larger in 16-pair lines than in 4- and 8-pair lines. In the second phase of selection (>14 generations), h_R² declined significantly (P<.01) in all lines, and only the I16 and M16 lines had h_R² values significantly (P<.01) greater than zero. Realized genetic correlations involving number born, 12-day litter weight, weaning weight and six-week weight tended to decline in the second phase of selection. The I16, M16 and control (C16) replicates were crossed in all combinations at generation 14. Crosses were then selected within litters for high postweaning gain. The h_R² values in the crossbred lines were all larger than those in the second selection phase for M16-1, M16-2 and I16-1, but not for I16-2. Within each N_e level, total response was significantly (P<.01) less for I lines compared with M lines. Total response increased as N_e increased, within each level of i. Relatively small differences in realized i values among N_e lines could not account for this result. The difference in total response among the N_e lines at a given selection intensity may be due to inbreeding depression and a combination of interactions involving "drift" and selection. By crossing replicates of the M lines with the C16 control, the effects of inbreeding depression were removed. Inbreeding depression and genetic drift, as defined herein, were equally important in accounting for differences among N_e lines in total response.     

Finding the Missing Link between Landscape Structure and Population Dynamics: A Spatially Explicit Perspective

We construct and explore a general modeling framework that allows for a systematic investigation of the impact of changes in landscape structure on population dynamics. The essential parts of the framework are a landscape generator with independent control over landscape composition and physiognomy, an individual-based spatially explicit population model that simulates population dynamics within heterogeneous landscapes, and scale-dependent landscape indices that depict the essential aspects of landscape that interact with dispersal and demographic processes. Landscape maps are represented by a grid of 50x50 cells and consist of good-quality, poor-quality, or uninhabitable matrix habitat cells. The population model was shaped in accordance to the biology of European brown bears (Ursus arctos), and demographic parameters were adjusted to yield a source-sink configuration. Results obtained with the spatially explicit model do not confirm results of earlier nonspatial source-sink models where addition of sink habitat resulted in a decrease of total population size because of dilution of high-quality habitat. Our landscape indices, which describe scale-dependent correlation between and within habitat types, were able to explain variations in variables of population dynamics (mean number of females with sink home ranges, mean number of females with source home ranges, and mean dispersal distance) caused by different landscape structure. When landscape structure changed, changes in these variables generally followed the corresponding change of an appropriate landscape index in a linear way. Our general approach incorporates source-sink dynamics as well as metapopulation dynamics, and the population model can easily be modified for other species groups.     

Effects of Grazer Presence on Genetic Structure of a Phenotypically Diverse Diatom Population

Studies of predator–prey systems in both aquatic and terrestrial environments have shown that grazers structure the intraspecific diversity of prey species, given that the prey populations are phenotypically variable. Populations of phytoplankton have traditionally considered comprising only low intraspecific variation, hence selective grazing as a potentially structuring factor of both genetic and phenotypic diversity has not been comprehensively studied. In this study, we compared strain specific growth rates, production of polyunsaturated aldehydes, and chain length of the marine diatom Skeletonema marinoi in both grazer and non-grazer conditions by conducting monoclonal experiments. Additionally, a mesocosm experiment was performed with multiclonal experimental S. marinoi populations exposed to grazers at different levels of copepod concentration to test effects of grazer presence on diatom diversity in close to natural conditions. Our results show that distinct genotypes of a geographically restricted population exhibit variable phenotypic traits relevant to grazing interactions such as chain length and growth rates. Grazer presence affected clonal richness and evenness of multiclonal Skeletonema populations in the mesocosms, likely in conjunction with intrinsic interactions among the diatom strains. Only the production of polyunsaturated aldehydes was not affected by grazer presence. Our findings suggest that grazing can be an important factor structuring diatom population diversity in the sea and emphasize the importance of considering clonal differences when characterizing species and their role in nature.     

Ecological Specialization in a Spatially Structured Population of the Thermophilic Cyanobacterium Mastigocladus laminosus

Laboratory evolution experiments suggest the potential for microbial populations to contribute significant ecological variation to ecosystems, yet the functional importance of genetic diversity within natural populations of microorganisms is largely unknown. Here, we investigated the distribution of genetic and phenotypic variation for a population of the cyanobacterium Mastigocladus laminosus distributed along the temperature gradient of White Creek, Yellowstone NP. A total of 153 laboratory strains were directly isolated from five sites with mean annual temperatures ranging between 39 and 54°C. Genetic characterization at four nitrogen metabolism genes identified 15 closely related lineages in the population sample. These lineages were distributed nonrandomly along White Creek, but the observed geographic structure could not be explained by limited dispersal capabilities. Temperature performance experiments with six M. laminosus lineages that maximized their respective relative abundances at different positions along the gradient provided evidence for niche differentiation within the population. Niche differentiation included a tradeoff in performance at high and low temperatures, respectively. The physiological variation of these lineages in laboratory culture was generally well matched to the prevailing temperature conditions experienced by these organisms in situ. These results suggest that sympatric diversification along an ecological selection gradient can be a potent source of evolutionary innovation in microbial populations.     

Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm

Pseudomonas putida strain MnB1, a biofilm-forming bacterial culture, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of aqueous Mn⁺² [Mn⁺²_(aq)] by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm, using scanning transmission X-ray microscopy (STXM) combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Mn L_2,3 absorption edges. Subsamples were collected from growth flasks containing 0.1 and 1 mM total Mn at 16, 24, 36, and 48 h after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at a 40-nm resolution. Manganese NEXAFS spectra were extracted from X-ray energy sequences of STXM images (stacks) and fit with linear combinations of well-characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III), and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn⁺²_(aq) was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission X-ray microscopy is a promising tool for advancing the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.