Similar Bird Communities Across Grazing Systems in the Nebraska Sandhills

Much of the remaining native rangeland in the Great Plains in the United States is privately owned and managed for beef production, and this single priority for land use may be contributing to declining avian biodiversity through a loss of structural heterogeneity. One proposed solution is to use multiple grazing systems across ranches, under the assumption that this approach will increase heterogeneity of vegetation structure and avian diversity across the landscape. We tested the relationship between grazing systems and avian diversity in the Nebraska Sandhills during 2014 and 2015 on a landscape that included 11 management units containing 5 different grazing systems. We used multivariate models to examine the relationship of bird diversity and communities to grazing systems at the management unit scale, and we used simulations to combine empirical data from ≥1 grazing system into virtual landscapes to test the hypothesis that multiple grazing systems would result in greater heterogeneity. The 5 most common avian species made up 84% of observations (28 species), and songbird richness was 5–6 species/7.06 ha at 53% of our plots. Variation in each of the diversity measures (Shannon diversity range = 0.41–2.2, Simpson's diversity range = 0.24–0.88) was best explained by the previous dormant season's stocking rate, and richness declined by about 1 species/plot with an increase in 1 animal unit month (AUM)/ha. Songbird community structure showed the most variance between management unit, but grazing system explained little community variation. None of the simulated landscapes consistently had greater structural heterogeneity of visual obstruction reading, litter depth, and cover of bare ground than others, and there was a limited level of heterogeneity overall in the simulated landscapes. In contrast to our predictions, a variety of grazing systems did not increase heterogeneity of vegetation structure across the landscape. Thus, conservation practitioners should encourage the use of other strategies to create structural heterogeneity, such as prescribed fires and extreme stocking rates, which will support a diverse grassland songbird community (i.e., a greater variety of bird species) across the landscape. © 2020 The Wildlife Society.     

Deep-Sea Macrobenthic Communities at Contrasting Sites off Portugal,Preliminary Results: II Spatial Dispersion

Small-scale, biogenic processes are thought to be important in creating a mosaic of microhabitats that allow co-existence of the large numbers of rare species found in deep-sea sediments. However, the large-scale effects of hydrodynamic disturbance seem likely to be important in high-energy settings on the deep-sea bed. This is investigated by examining spatial dispersion patterns in the macrobenthic populations at two deep-sea sites off Portugal. The widely differing conditions of sediment disturbance at the two sites are related to differences in macrobenthic species diversity and dominance. Closely grouped, transponder-mapped, replicate box core samples, each divided into 25 “vegematic” subcores permitted analysis of dispersion patterns at two spatial scales at each site. One site was located on the Tagus Abyssal Plain (TAP), and the other in the nearby Setubal Canyon (SC) where ripple bedforms indicate vigorous bed flow, probably with a tidal periodicity. Greater aggregation at the scale of tens of metres is indicated from the observed numbers of SC species per box core being wide underestimates of the value predicted by rarefaction of the pooled total compared to those from TAP. Variance/mean ratios for individual species of bivalves and tanaids indicated more aggregation in spatial distribution between box cores from SC than from TAP. Dispersion chi-square analysis also indicated more non-randomness at SC between box cores than for the TAP cores. However, low faunal abundances in the TAP samples render the results of analyses for this site somewhat inconclusive and therefore the trend indicating less aggregation at TAP compared to SC must be regarded as weak for the groups examined. Analyses of the distribution of tanaids, and bivalves at a 100 × 100 mm subcore scale showed no convincing significant departure from random expectation, but low abundances in these groups reduces the sensitivity of the tests applied. Between-core aggregation detected at SC may reflect habitat variation resulting from the varying depth within the area of sampling, while within-core patchiness could be influenced by the ripple bed forms on the sediment.     

Deep-Sea Macrobenthic Communities at Contrasting Sites off Portugal,Preliminary Results: I Introduction and Diversity Comparisons

Species diversity, faunal composition and abundance in the deep-sea macrobenthos are investigated at two, adjoining deep-sea areas off Portugal experiencing contrasting hydrodynamic conditions in order to test for the importance of disturbance in structuring the community. The first was located at 5,035 m depth on a presumably low current-energy site on the Tagus Abyssal Plain (TAP) and the second was centered in the lower end of the Setubal Canyon (SC) at 3,400 m depth where high levels of hydrodynamic activity are inferred from ripple bedforms visible in sea bed photographs. Closely grouped, transponder-mapped, “vegematic” box core samples were taken at each site. Agglutinated foraminifers numerically dominate the macrofauna (retained by 300 μm sieve) at both sites. Seagrass content in the SC cores indicates downslope detrital input from shallow water which is absent in the TAP samples. This must contribute, possibly with high levels of resuspended particles in near-bed flow, to the almost tenfold difference in abundance of metazoan macrofauna at the two sites. Expected species diversity measured from rarefaction is highest at TAP, both for pooled data and when foraminifers. tanaids and bivalve are considered separately. Evenness (equitability) in species' abundances is also higher at TAP than at SC. These differences are compared with benthic community data from the hydrodynamically disturbed High Energy Benthic Boundary Layer (HEBBLE) site on the Nova Scotia continental rise, and from the Rockall Trough (N.E. Atlantic). In common with these sites, strong bed flow at SC is thought to result in relatively high abundances, lower species richness and greater unevenness by acting to periodically disturb and reduce populations. Differences in the degree to which different faunal groups seem to be affected might be related to differences in lifestyle, particularly burrowing depth.     

Microbial Communities in Sunken Wood Are Structured by Wood-Boring Bivalves and Location in a Submarine Canyon

The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of Xylophaga, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of Xylophaga spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that Xylophaga spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of Xylophaga spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life.     

Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano

We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon–Wiener diversity index H was higher for Bacteria (1.92–4.03) than for Archaea (0.99–1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex Bacteria community consisted of 20 phylogenetic groups at the phylum/candidate division level. Proteobacteria, in particular δ-Proteobacteria, was the dominant group. In most sediment layers, the dominant phylotypes of both the Archaea and Bacteria communities were found in neighbouring layers, suggesting some overlap in species richness. The similarity of certain prokaryotic communities was also depicted by using four different similarity indices. The direct comparison of the retrieved phylotypes with those from the Kazan mud volcano of the same field revealed that 40.0% of the Archaea and 16.9% of the Bacteria phylotypes are common between the two systems. The majority of these phylotypes are closely related to phylotypes originating from other mud volcanoes, implying a degree of endemicity in these systems.     

Variation in the Pattern of Nucleotide Substitution Across Sites

A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed. We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio testing indicated that a model that allows variation in the transition/transversion rate bias across sites provided a significant improvement in fit for most protein coding genes but not for the pseudogene. When the analysis was repeated with parameters estimated separately for first, second, and third codon positions, strong heterogeneity was uncovered for the first and second codon positions; the variation in the transition/transversion rate was generally weaker at the third codon position. The transition rate bias and branch lengths are underestimated when variation in the transition/transversion rate was not accommodated, suggesting that it may be important to accommodate variation in the pattern of nucleotide substitution for accurate estimation of evolutionary parameters. Received: 4 November 1997 / Accepted: 19 May 1998     

粤北六地森林群落的比较研究

利用植被样方法和重要值计算,对地处广东北部山区的南雄青嶂山、始兴南山、曲江沙溪、翁源青云山、新丰云髻山、河源大桂山的森林群落乔木层优势科、优势种及各地共优种的径级结构进行了比较分析。结果表明,各地共有优势科为壳斗科、樟科、山茶科、金缕梅科、冬青科、杜鹃花科等13科,与他们所处的中亚热带地理位置相适应;6地共有优势种9个,优势度存在明显差异。群落的相似性系数以沙溪与南山之间的75．88％为最大;青云山与大桂山之间的45．64％为最低;南山与其他各地的群落相似性系数均大于60％。共有优势种的种群径级结构中,甜锥（Castanopsis eyrei）、罗浮柿（Diospyros morrisiana）、酸枣（Choerospondias axillaris）种群在粤北6地的个体数量分布,与各地的纬度差异有较明显的相关性。云髻山和沙溪的黧蒴（Castanopsis fissa）种群呈增长趋势,而南山和大桂山的趋于衰退。青云山的木荷（Schima superba）种群呈增长趋势,而其他地区的更新不良。黄樟（Cinnamomum porrectum）在各地分布为散生,种群规模小,径级结构不完整。各地枫香（Liquidambar formosana）种群的径级结构不完整,缺乏Ⅰ级幼苗。杉木（Cunninghamia lanceolata）、马尾松（Pinus massoniana）种群在粤北6地均呈现衰退趋势。研究结果提示,整体上粤北6地森林的非地带性植被趋于衰退,常绿阔叶林的恢复进展顺利。     

Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.     

A Hypothetical Application of the Pollution-Induced Community Tolerance Concept in Megafaunal Communities Found at Contaminated Sites

The purpose of our paper is to suggest a novel, hypothetical and yet untested use of the pollution-induced community tolerance concept (PICT). Historically, PICT has been applied to determine whether toxicants are deleterious in microfaunal aquatic and terrestrial communities. We hypothesize that it may be possible to apply PICT to megafaunal organisms (e.g., vertebrates). In doing so, researchers could (1) identify which toxicant, in a complex mixture of toxicants, is harmful since only those contaminants that exert selection pressure are biologically relevant and will result in changes in community structure and (2) determine the transfer of toxicants across trophic levels found within that community. We suggest that community tolerance could be measured in megafaunal communities by measuring biomarkers of exposure and effect in either a number of individuals that make up different populations of animals comprising a community, or in the community as a whole. In this article we discuss the theoretical suitability of our megafaunal PICT approach to the assessment of contaminated sites and some of the potential pitfalls associated with its use. Our intention is that this paper will generate debate and commentary surrounding PIGT and its potential uses in the future. Whether this potential approach is feasible remains to be determined.     

Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray

PhyloTrac is an integrated desktop application for analysis of PhyloChip microarray data. PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archaeal communities in complex environmental samples. PhyloTrac is free for noncommercial organizations and is available for all major operating systems at http://www.phylotrac.org/.The PhyloChip is a low-cost Affymetrix GeneChip microarray, developed at Lawrence Berkeley National Laboratory (LBNL), designed to detect and quantify abundance of bacterial and archaeal taxa using signature probes targeting all known 16S rRNA gene sequences. The second generation of the PhyloChip microarray targets nearly 9,000 operational taxonomic units (OTUs), with an average of 24 probes, each 25 bp long, and the upcoming third-generation PhyloChip application will target an even larger number of OTUs. Multiple, complex environments have been successfully analyzed using the PhyloChip microarray, including, among others, air (2), soil (1), the human lung (6), and the gut (9). PhyloChip microarrays are manufactured by Affymetrix, but to date, analysis has been available only from within LBNL, limiting the accessibility of the technology. PhyloTrac addresses this limitation by providing a standardized analysis package for the PhyloChip microarray, including microarray normalization, OTU quantification, multiple interactive visualizations, and integrated analytics.     

重组GST-HBx蛋白在表达过程中断裂状况的研究

目的 在对乙型肝炎病毒非结构蛋白HBx研究的过程中,发现体外表达HBx蛋白产物的稳定性存在差异.为了了解其中的原因,拟通过原核表达方式进行分析.方法 以包含全长HBV DNA的质粒pEco63为模板,通过PCR反应,扩增HBV X基因全长序列（1～154氨基酸）和截短序列（48～104氨基酸,48～146氨基酸,98～146氨基酸）,将这几种不同长度和位置的HBX DNA序列克隆到pGEX4T-2原核表达载体中,并通过下游引物设计中引入6×组氨酸标签序列.结果 最终成功构建N端融合GST蛋白标签序列和C端融合6×组氨酸标签序列的4种HBx重组表达载体.将4种包含不同长度HBx的重组质粒转化大肠埃希菌Rosetta,培养至菌液浓度A值大约0.6左右,加入终浓度0.1 mmol/L的IPTG进行诱导表达.提取全菌蛋白通过Western印迹对HBx各重组蛋白产物的N端和C端进行检测.结论 在分段表达的HBx重组蛋白中发生了多处局部的断裂,而断裂部位主要集中于GST蛋白上.而造成这一结果的原因可能与HBx蛋白功能区域暴露后与GST相互作用有关.     

NMR Study of Chloroplast Water in Acer platanoides: Water Exchange at Membrane-Bound Sites and Across the Chloroplast Envelope Membrane

Abstract: Nuclear magnetic resonance (NMR) spin relaxation techniques were used to measure the rate of water exchange across the chloroplast envelope membrane and to detect exchange of water-hydrogens between the bound and fluid states in Acer platanoides shade leaves. Results indicate that individual water molecules resided within a chloroplast for 320 ± 65 ms, on average, before exchanging through the envelope, and that exchangable bound hydrogens are at least six times more abundant in the chloroplast than in the nonchloroplast compartments.     

Greenhouse Gas Balance of Sphagnum Farming on Highly Decomposed Peat at Former Peat Extraction Sites

Ecosystems - For two years, we quantified the exchange of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) at two different large-scale Sphagnum farming sites. At both, peat extraction...     

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.     

Prediction of Substrate Removal Rates of Attached Microorganisms and of Relative Contributions of Attached and Suspended Communities at Field Sites

A mathematical model composed of a direct proportionality relationship between bulk water velocities and field-determined second-order microbial transformation rate coefficients, and the relative rate coefficient of a benchmark chemical, was developed for estimating the substrate removal rates of rapidly degraded chemicals by attached organisms in shallow (<1 m deep) aquatic ecosystems. Data from 31 field experiments involving the addition of 2,4-dichlorophenoxyacetic acid methyl ester (2,4-DME) in nine field areas were used to determine a field-derived second-order rate coefficient for microbial transformation of the ester. By using 2,4-DME as a benchmark chemical, the model was used to predict microbial transformation rates of the butoxyethyl ester of 2,4-dichlorophenoxyacetic acid (2,4-DBE) at five other field sites. The predicted half-lives of 2,4-DBE varied 1,500-fold and were within about a threefold range or less of the measured half-lives. Under conditions of mass transport limitation, the contributions of attached microorganisms relative to total microbial activities at various field sites were related to the ratio of water velocity, U, and depth, D, showing that historical definitions of ecosystems according to flow and depth characteristics are also valid for describing the process-related structure of ecosystems. An equation was developed for predicting the relative contributions of attached and suspended communities with values of U and D for lotic and lentic ecosystems. On the basis of this equation, attached microorganisms were expected to be insignificant in deep lentic ecosystems and suspended microorganisms were expected to be insignificant in shallow lotic systems for the same process carried out by both populations. Neglecting epiphytic microorganisms, both suspended and attached organisms were expected to be significant in wetlands.     

木材上的微生物类群对木材的分解及其演替规律

论述了木材上的微生物类群以及各类群在木材生物分解过程中的演替规律 ,并解释了活立木心材能够发生腐朽的原因。结果表明 :能够生长在木材上的微生物类群有木材腐朽菌、木材软腐菌、木材变色菌、污染性霉菌、细菌、放线菌等多种。这些微生物类群共同合作完成对复杂的木质有机物质的生物分解。它们按一定次序进行作用 ,在木材生物分解的不同时期显示出明显的菌种协调与演替规律。一般情况是细菌、一些半知菌、接合菌和子囊菌等先驱微生物首先侵入 ,然后草本对策的木材腐朽菌开始出现 ,最后由竞争对策或忍耐对策的木腐菌取代草本对策的木腐菌 ,这时木材的分解过程就进入稳定的发展阶段 ,最后使木材分解或腐朽。木材腐朽最终是腐殖化阶段 ,这时微生物群落被土壤习居菌如毛霉、青霉、木霉、镰刀菌及细菌与放线菌等所取代。     

Microbial Communities in the Chemocline of a Hypersaline Deep-Sea Basin (Urania Basin, Mediterranean Sea)

The Urania basin is a hypersaline sulfidic brine lake at the bottom of the eastern Mediterranean Sea. Since this basin is located at a depth of ~3,500 m below the sea surface, it receives only a small amount of phytoplankton organic carbon. In the present study, the bacterial assemblages at the interface between the hypersaline brine and the overlaying seawater were investigated. The sulfide concentration increased from 0 to 10 mM within a vertical interval of 5 m across the interface. Within this chemocline, the total bacterial cell counts and the exoenzyme activities were elevated. Employing 11 cultivation methods, we isolated a total of 70 bacterial strains. The 16S ribosomal DNA sequences of 32 of the strains were identical to environmental sequences detected in the chemocline by culture-independent molecular methods. These strains were identified as flavobacteria, Alteromonas macleodii, and Halomonas aquamarina. All 70 strains could grow chemoorganoheterotrophically under oxic conditions. Sixty-six strains grew on peptone, casein hydrolysate, and yeast extract, whereas only 15 strains did not utilize polymeric carbohydrates. Twenty-one of the isolates could grow both chemoorganotrophically and chemolithotrophically. While the most probable numbers in most cases ranged between 0.006 and 4.3% of the total cell counts, an unsually high value of 54% was determined above the chemocline with media containing amino acids as the carbon and energy source. Our results indicate that culturable bacteria thriving at the oxic-anoxic interface of the Urania basin differ considerably from the chemolithoautotrophic bacteria typical of other chemocline habitats.