Avian use of perennial biomass feedstocks as post-breeding and migratory stopover habitat

Increased production of biomass crops in North America will require new agricultural land, intensify the cultivation of land already under production and introduce new types of biomass crops. Assessing the potential biodiversity impacts of novel agricultural systems is fundamental to the maintenance of biodiversity in agricultural landscapes, yet the consequences of expanded biomass production remain unclear. We evaluate the ability of two candidate second generation biomass feedstocks (switchgrass, Panicum virgatum, and mixed-grass prairie) not currently managed as crops to act as post-breeding and fall migratory stopover habitat for birds. In total, we detected 41 bird species, including grassland specialists and species of state and national conservation concern (e.g. Henslow's Sparrow, Ammodramus henslowii). Avian species richness was generally comparable in switchgrass and prairie and increased with patch size in both patch types. Grassland specialists were less abundant and less likely to occur in patches within highly forested landscapes and were more common and likely to occur in larger patches, indicating that this group is also area-sensitive outside of the breeding season. Variation in the biomass and richness of arthropod food within patches was generally unrelated to richness and abundance metrics. Total bird abundance and that of grassland specialists was higher in patches with greater vegetation structural heterogeneity. Collectively, we find that perennial biomass feedstocks have potential to provide post-breeding and migratory stopover habitat for birds, but that the placement and management of crops will be critical factors in determining their suitability for species of conservation concern. Industrialization of cellulosic bioenergy production that results in reduced crop structural heterogeneity is likely to dramatically reduce the suitability of perennial biomass crops for birds.     

Small- and large-scale effect of the SW Atlantic burrowing crab Chasmagnathus granulatus on habitat use by migratory shorebirds

Here we address the question of whether the presence of the burrowing crabs Chasmagnathus granulatus affects small- and large-scale habitat use by migrant shorebirds. This crab is the dominant species in soft bare sediments and vegetated intertidal areas along the SW Atlantic estuaries (southern Brazil 28°S to the northern Argentinean Patagonia 42°S). They generate very extensive burrow beds in soft bottom intertidal areas. Our information shows that this burrowing crab affects the small-scale habitat use by shorebirds, given that shorebirds never walk through the funnel-shaped entrances of burrows. Given that crab burrow entrances occupy up to 40% of the intertidal area, there is a large decrease of available shorebird habitat in crab beds, restricting their activity to the spaces between the burrows. The southern migratory shorebird Charadrius falklandicus maximize the use of these areas by foraging closer to the burrows than the other bird species. Neotropical migrants, such as Calidris fuscicollis, Pluvialis squatarola and Tringa melanoleuca, used foraging paths that tended to maximize the distance from burrows, especially the distance to larger burrows. A field experiment showed that this was not necessarily due to a decrease in the availability of polychaetes near the crab burrows. A combination of landscape measurements and satellite images showed that crab beds covered up to 40% of the intertidal area of the Mar Chiquita coastal lagoon (37°40′S, Argentina), and nearly 100% of the intertidal area of the Bahia Blanca estuary (38°48′-39°25′S, Argentina). These two estuaries are located along the migratory flyway of Neotropical migratory shorebirds, but the Bahia Blanca estuary (area∼110,000 ha) shows a much lower shorebird diversity than Mar Chiquita (area∼4500 ha). The most common species in Bahia Blanca is the two-banded plover C. falklandicus, the species least affected by crabs at Mar Chiquita and which prefers to use high-density crab areas as foraging sites. The oystercatcher Haematopus palliatus was also most abundant in high-density crab areas, but they used these areas for resting. The abundances of preys varied during the study period and between the crab density areas, indicating that the use of these areas by birds is independent of crab density. However, burrowing crabs affect the depth distribution of polychaete and thus their availability to shorebirds. We suggest that this shorebirds-burrowing organism interaction could be generalized for other intertidal estuarine habitats.     

低温微生物适冷特性及其在食品工业中的潜在用途

温度是影响生物生存的一个限制因素。所有微生物都具有一特征性的最适生长温度 ,此时它们具有最大的生长和繁殖速率。同时 ,微生物还具有一定的温度耐受范围 ,低于或高于这一生长温度范围的限度 ,它们就会因新陈代谢失活而不能生长。按照在不同温度条件下生长能力的不同 ,微生物可被大致分为 3类 :高温菌、中温菌和低温菌。其中低温菌又通常被分为嗜冷菌 (ｐｓｙｃｈｒｏｐｈｉｌｅｓ)和耐冷菌 (ｐｓｙｃｈｒｏｔｒｏｐｈｓ)。按照Ｍｏｒｉｔａ( 1 975 )的定义 ,嗜冷菌的最适生长温度 <1 6℃ ,其生长温度的上限为 2 0℃ ;耐冷菌则是指能在 0…     

Shifts in morphometrics and their relation to hydrodynamic potential and habitat use during grayling ontogenesis

The theory of saltatory ontogeny predicts sudden morphological shifts during fish development which often occur simultaneously with physiological, anatomical or behavioural shifts. Therefore, our objectives were to identify potential sudden morphological shifts during grayling Thymallus thymallus ontogenesis and to check if these shifts affected the hydrodynamic potential of grayling in periods of known shifts in habitat use. In the 144 grayling studied (total length: 14·9–142·7 mm), three of 28 morphological variables considered revealed saltatory events during ontogenesis: position of maximal body height, position of maximal body width, and length to pelvic fin insertion. Using all variables (except total and standard length), five morphological groups were separated by multivariate analysis and each group had a particular hydrodynamic potential related to the drag of flow. Between these five different morphological groups, differences in the physical habitat use were observed. Basically, the saltatory pattern during grayling ontogenesis corresponded to a sequential habitat use that increased flow exposure and, simultaneously, to a stepwise improvement (at each habitat shift) of the hydrodynamic potential until the body had a shape that minimized drag of flow. The study confirms the theory of saltatory ontogeny for grayling in a context of flow physics and hydrodynamic adaptations.     

Accumulation of metals in Anguilla anguilla from the Tagus estuary and relationship to environmental contamination

Accumulation of metals (Cd, Cu, Hg, Pb and Zn) in the liver and muscle of the European eel, (Anguilla Anguilla), the influence of sex and size on tissue contamination, and the potential use of this species as a pollution biomonitor in the Tagus estuary were investigated. A total of 90 eels were captured in spring 2007 from six sampling stations. Metal concentrations were higher in the liver, except for Hg, which showed higher levels in the muscle. No significant differences were found between sexes in contrast to what was obtained in the size classes (TL < 240 mm, 240 mm ≤ TL < 350 mm and TL ≥ 350 mm). No clear relationships could be established between concentrations of metals in sediment and tissues, mainly due to the general heterogeneity in environmental conditions among stations, which hinders the use of this species as a biomonitor for metals contamination in this estuary.     

Charcoal as a habitat for microbes and its effect on the microbial community of the underlying humus

Wildfires produce a charcoal layer, which has an adsorbing capacity resembling activated carbon. After the fire a new litter layer starts to accumulate on top of the charcoal layer, which liberates water‐soluble compounds that percolate through the charcoal and the unburned humus layer. We first hypothesized that since charcoal has the capacity to adsorb organic compounds it may form a new habitat for microbes, which decompose the adsorbed compounds. Secondly, we hypothesized that the charcoal may cause depletion of decomposable organic carbon in the underlying humus and thus reduce the microbial biomass. To test our hypotheses we prepared microcosms, where we placed non‐heated humus and on top one of the adsorbents: non‐adsorptive pumice (Pum), charcoal from Empetrum nigrum (EmpCh), charcoal from humus (HuCh) or activated carbon (ActC). We watered them with birch leaf litter extract. The adsorbing capacity increased in the order Pumorg in the litter extract, respectively. After one month, all adsorbents harboured microbes, but their amount and basal respiration was largest in EmpCh and HuCh, and smallest in Pum. In addition, different kinds of microbial communities with respect to their phospholipid fatty acid and substrate utilization patterns were formed in the adsorbents. The amount of microbial biomass and number of bacteria did not differ between humus under different adsorbents, although different microbial communities developed in humus under EmpCh compared with Pum, which is obviously related to the increased pH of the humus under EmpCh, and also ActC. We suggest that charcoal from burning can support microbial communities, which are small in size but have a higher specific growth rate than those of the humus. Although the charcoal layer induces changes in the microbial community of the humus, it does not reduce the amount of humus microbes.     

木质纤维素分解复合菌系WSD-5组成菌株的分离及其产酶特性

复合菌系WSD-5具有高效的分解能力和产酶能力,以探明WSD-5的协同分解机理和优化高效组合为目的,通过纯培养分离手段,获得了11株细菌和3株真菌。16S rDNA比对结果表明,细菌分别为Pseudomonas sp.、Pseudomonas aeruginosa、Achromobacter sp.、Stenotrophomonas sp.、Bacillus fusiformis、Bacillus cereus、Brevundimonas sp.、Ochrobactrum sp.、Cytophaga sp.、Benzo(a)pyrene-degrading bacter、Flavobacterium sp.的近缘种;26S rDNA比对结果表明3株真菌分别为Pseudallescheria boydii、Coprinus cinereus的近缘种。分离菌株中有4株细菌和3株真菌能在CMC平板上产生透明圈,但以糖化力法测定酶活结果只有3株真菌具有产酶能力。3株真菌的酶活动态测定结果,酶活的高峰均出现在7?14 d,并且呈现多峰变化;3株真菌的酶活种类表现为,滤纸酶活性、纤维素内切酶活性和外切酶活性均以菌株F1最高,分别达到了1.05、5.53和0.56 U/mL,β-葡萄糖甘酶活性和木聚糖酶活性以菌株FC最高,分别达到0.44和58.95 U/mL,其木聚糖酶活为F1最高值的6倍。     

Ecology of Dolichopodidae (Diptera) in a wetland habitat and their potential role as bioindicators

Ecological investigations of long-legged flies (Dolichopodidae) were carried out in wet meadow wetlands near České Budějovice, Czech Republic. Sampling was performed during the adult flies’ seasonal activity (March–October) in 2002, 2003 and 2004 using yellow pan traps, Malaise traps, emergence traps, and by sweeping. Altogether 5,697 specimens of 78 species of Dolichopodidae were collected, identified and analysed. The study examined community structure, species abundance, and diversity (Shannon-Weaver’s index - H’; Sheldon’s equitability index - E). Chrysotus cilipes, C. gramineus and Dolichopus ungulatus were the most abundant species in all three years. Species richness and diversity seem strongly affected by soil moisture.     

Monitoring of horizontal gene transfer from agricultural microorganisms to soil bacteria and analysis of microbial community in soils

To investigate the possibility of horizontal gene transfer between agricultural microorganisms and soil microorganisms in the environment, Bacillus subtilis KB producing iturin and the PGPR recombinant strain Pseudomonas fluorescens MX1 were used as model microorganisms. The soil samples of cucumber or tomato plants cultivated in pots and the greenhouse for a six month period were investigated by PCR, real-time PCR, Southern hybridization, and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Our data from Southern blotting and TRFLP patterns suggest that the model bacteria do not give significant impacts on the other bacteria in the pots and greenhouse during cultivation.     

Fish habitat use response to anthropogenic induced changes of physical processes in the Elwha estuary, Washington, USA

The Elwha River estuary has been significantly influenced by anthropogenic changes to the river, including two large dams upriver and rock dikes installed in the estuary. Together these have disrupted hydrodynamic processes and subsequent sediment delivery throughout the watershed. This article defines the functional response of fish distribution within the estuary as a result of these changes. We assessed fish distribution of three main areas of the Elwha estuary using standard beach seining techniques from March to August 2007. Species composition, ecological indices, and relative proportion of all salmonids, and in particular Chinook salmon (Oncorhynchus tshawytscha), were consistently significantly different across the estuary. Differences corresponded to a rock dike installed 30 years ago, and a sediment lens that was observed to form at the entrance to the east estuary. Sediment lenses are documented to be a common occurrence in the Elwha nearshore, and symptomatic of documented, severely disrupted sediment processes of the Elwha River. Combining the fish distribution documented in this study with the rock dike and observed sediment lens and the sediment processes documented by other researchers we, therefore, conclude: (1) Fish use within the Elwha River estuary is complex, and even fragments of connected estuary are critically important for migrating salmon; (2) Anthropogenic effects, including in river damming and diking of the estuary, can be an important ecological driver in nearshore habitat function that should be appropriately considered in estuary habitat research, management, and restoration; and (3) Juvenile salmonids appear to be able to respond to dynamic sediment environments if there are habitat options available.     

模拟氮沉降对中亚热带米槠天然林土壤解磷微生物群落和功能潜力的影响

解磷微生物是森林土壤磷循环的关键驱动因素,对亚热带低磷土壤尤为重要。由于微生物对环境变化较为敏感,氮沉降下土壤微生物如何变化以及如何影响土壤磷有效性尚不清楚。为此,依托福建三明森林生态系统与全球变化国家野外科学观测研究站建立的米槠天然林长期氮沉降观测平台,借助16S rRNA和ITS高通量测序以及PICRUSt功能预测方法,探索氮添加对土壤解磷微生物群落和功能潜力的影响。结果表明:氮添加显著增加了土壤有效氮含量,但显著降低了Resin-P、NaHCO₃-P和TPo,表明氮沉降改变了土壤养分平衡,加剧了磷限制。此外,氮添加降低了根瘤菌和伯克霍尔德菌等解磷细菌的丰度,却增加了青霉菌和曲霉菌等解磷真菌的丰度。PICRUSt功能预测进一步发现,存在15种能够编码磷酸酶的基因,并且与对照相比,施氮后酸性磷酸酶、碱性磷酸酶和植酸酶等酶基因丰度显著增加。综上,本研究发现施氮加剧了亚热带米槠天然林土壤的磷限制,同时增加了解磷真菌的丰度和磷酸酶的基因丰度来促进有机磷矿化,这可能是氮沉降下驱动米槠天然林土壤磷转化的主要微生物机制。     

Evaluation of bacterial aerotaxis for its potential use in detecting the toxicity of chemicals to microorganisms

Bacterial aerotaxis (the movement of a cell toward oxygen) was evaluated for its potential use in detecting the toxicity of chemicals to microorganisms. The level of toxicity was determined by the concentration of test chemicals resulting in a 50% inhibition of aerotaxis of Pseudomonas aeruginosa PAO1 after 40 min of exposure. The aerotactic responses of P. aeruginosa were measured by using chemotaxis well chambers. Each clear acrylic chamber had a lower and upper well separated by a polycarbonate filter with a uniform pore size of 8.0 microm. To automatically detect bacterial cells that crossed the filter in response to a gradient of oxygen, P. aeruginosa PAO1 was marked with green fluorescent protein (GFP), and the GFP fluorescence intensity in the upper well was continuously monitored by using a fluorescence spectrometer. By using this technique, volatile chlorinated aliphatic compounds, including trichloroethylene (TCE), trichloroethane, and tetrachloroethylene, were found to be inhibitory to bacterial aerotaxis, suggesting their possible toxicity to microorganisms. We also examined more than 20 potential toxicants for their ability to inhibit the aerotaxis of P. aeruginosa. Based on these experimental results, we concluded that bacterial aerotaxis has potential for use as a fast and reliable indicator in assessing the toxicity of chemicals to microorganisms.     

The relationship between the microbial activity of the autochthonous microorganisms of pristine and contaminated soils and their potential for the degradation of mineral oil hydrocarbons

The microbial activity of pristine and contaminated soils was investigated by measuring the following parameters: glucose induced respiration, dimethylsulphoxide reduction and the hydrolysis of fluorescein diacetate. The viable counts were determined by the plate count method. The ability of the autochthonous microorganisms of the investigated soils to degrade diesel fuel was determined in a closed system on the basis of the oxygen consumption and by direct measurements of the hydrocarbon concentrations. As expected, compost showed the highest microbial activity with regard to all three parameters, followed by the grassland and the arable soil samples which were also found to have high activity. However, soils that had been exposed to mineral oil for a long period of time showed significantly lower values. Microorganisms from contaminated sites had a high degradation potential; few pristine soils reached similar turnover rates. The investigations showed that the level of the degradation of diesel fuel in pristine soils correlated with their microbial activity, but this correlation was not found in the investigated contaminated soils.     

杭州湾及钱塘江河口南岸滨海湿地鸟类群落多样性及其对滩涂围垦的响应

为了解杭州湾及钱塘江河口区域围垦过程中多种人工湿地对于鸟类的作用及在快速的土地利用方式转变过程中鸟类的响应过程,2008年11月至2011年9月,作者对上虞曹娥江口至镇海甬江口沿岸滨海湿地鸟类资源进行调查,共记录鸟类16目52科220种,其中候鸟173种,占总数的78.6％,属于国家Ⅰ、Ⅱ级重点保护野生动物的24种.对研究区域的8种生境的鸟类群落组成、多样性及相似性进行了比较.结果表明,记录物种数较多的生境依次为芦苇水塘(95种,占总数的43.2％)、海涂林地(93种,占总数的42.3％)、自然潮间带和海涂水库(均为78种,各占总数的35.5％),其他生境的物种数均不少于67种(占总数的30.5％以上);从不同鸟类类群的分布看,82.5％的鸻鹬类分布在自然潮间带,69.2％的雁形目鸟类出现在海涂水库,73.4％的雀形目鸟类分布在海涂林地,海涂林地也是大量鹭鸟的繁殖场所;与自然潮间带相似性系数最高的生境依次为围垦滞留区、海涂水库和芦苇水塘,相似性系数分别为0.56、0.34和0.30;从整体上看,海涂林地和海涂水库的鸟类群落G-F指数最高,自然潮间带最低,但水鸟G-F指数最高的生境类型依次为围垦滞留区、海涂水库和自然潮间带.围垦是目前对杭州湾鸟类动态影响最大的人为干扰活动,适度围垦和合理的垦后土地利用方式可能提高整个区域的鸟类多样性水平.为了有效保护杭州湾鸟类多样性尤其是依赖自然潮间带的鸟类多样性,应加强对滩涂资源的保护与可持续利用;在滩涂围垦过程中应尽量保留足够数量和面积的高潮停歇地;同时,加强对围垦滞留区的水位管理,并注重营造适合鸟类栖息的类型多样的围区人工湿地系统.     

Diversity of terrestrial gastropod mollusks in the Pacific region of Nicaragua, and their habitat preferences

Diversity of terrestrial gastropod mollusks in the Pacific region of Nicaragua, and their habitat preferences. Landsnail communities of the Nicaraguan Pacific Slope were studied. The study area was subdivided into 21 quadrats (ca. 40 x 40 km). A high taxonomic richness was found: 79 species, 43 genera and 23 families. Species richness (S) per quadrat ranged from 17 through 50. The biogeographic index presented higher values on quadrats 5 (3.04), 6 (3.03), 8 (2.96) and 11(2.96). Quadrat 11 had the highest species richness (S=50), and one of the highest biogeographic index values (IB=2.96). Gastropod mollusk communities are favored by sites with an illumination of filtered sun, associated to riparian forests and with a susbtratum of wet soils and leaf litter.     

Diversity and occurrence of herbaceous communities in West African savannas in relation to climate,land use and habitat

In the face of the current changes in land use and climate as well as habitat destruction, it is important to study herbaceous vegetation as an indicator of changes occurring in savanna ecosystems. We investigated the effects of climate, land use and habitat, both alone and in combination, on the diversity and occurrence of West African savanna herbaceous plant communities. Floristic data and environmental variables were sampled in Burkina Faso and subjected to ordination and indicator species analysis to explore the variation in nine vegetation types. Regression analyses showed that climate, land use, humidity gradient, soil fraction and vegetation structure discriminate herbaceous plant communities. Climate, habitat and their interaction had the greatest effect on the occurrence of these communities. Changes in species richness of the studied communities were mainly due to climate, land use and their interaction, which were more important for increasing rather than decreasing diversity. In all cases, climate conditions remained the most important environmental factor driving vegetation variation in West African savannas. Beside this, the effects of habitat degradation in interaction with land use and climatic conditions indicate land use to be a threat for the diversity of the herbaceous vegetation.     

Rainfall and habitat interact to affect the condition of a wintering migratory songbird in The Bahamas

On the subtropical and tropical wintering grounds of migratory birds, variation in moisture levels and habitat can influence the availability of food resources and subsequently impact overwintering birds. Using stable carbon isotopes in blood samples as a measure of moisture, we assessed the interactive effects of rainfall, vegetation, and moisture on the demographics and condition of Prairie Warblers (Setophaga discolor) wintering in The Bahamas. Carbon isotopes in Prairie Warbler blood were more depleted in taller, wetter habitats; we additionally detected novel temporal effects of rainfall on isotope values. During a winter with more rainfall, most birds maintained mass and pectoral muscle regardless of the habitat type occupied. In a winter with less rainfall, birds lost mass and pectoral muscle, and this effect was more pronounced in birds with enriched isotope values and birds that occupied drier, shorter habitat. Prairie Warblers exhibited strong patterns of sexual habitat segregation with males disproportionately observed in areas with taller vegetation and females in shorter vegetation. During the drier winter, older males had better maintenance of pectoral muscle compared to females and younger individuals. Also in the drier winter, daily rainfall patterns explained more of the variation in body condition compared to the date of capture; pectoral muscle was best explained by recent precipitation (during the previous 30 days), while size‐corrected mass was more a function of longer‐term (90‐day) rainfall and habitat moisture. Our findings along with other studies suggest that Prairie Warblers and other migratory birds are sensitive to interactions between annual variation in winter rainfall, within‐season daily rainfall patterns, and habitat quality. Increasing drought and habitat loss in the Caribbean may be having a negative impact on wintering bird populations. To best conserve Nearctic–Neotropical migratory passerines in the region, we recommend prioritizing the protection of the least drought‐prone wintering areas.     

Analysis of the differences in microbial community structures between suspended and sessile microorganisms in rivers based on quinone profile

In this study, a quinone profiling method was applied to clarify the differences in community structure between suspended and sessile microorganisms in rivers. The compositions of microbial quinone of 6 sites for 4 rivers were analyzed. Ubiquinone (UQ)-8, UQ-10, menaquinone (MK)-7, and plastoquinone (PQ)-9 were observed in all samples of suspended and sessile microorganisms for the sites investigated. The dominant quinone species in suspended microorganisms was ubiquinone, and that in sessile microorganism was photosynthetic quinones (namely PQ-9 and vitamin K1). This indicated that aerobic bacteria were abundant in the suspended microorganisms, and photosynthetic microorganisms such as micro-algae and cyanobacteria dominated in the sessile microorganisms. The quinone concentration in the river waters tested, which reflects the concentration of suspended microorganisms, ranged from 0.045 to 1.813 nmol/L. The microbial diversities of suspended and sessile microorganisms calculated based on the composition of all quinones were in the range from 3.4 to 7.5, which was lower than those for activated sludge and soils. Moreover, the diversity of heterotrophic bacteria for sessile microorganisms in the rivers was higher than that for the suspended microorganisms.