Phylogenetic diversity of NO reductases,new tools for nor monitoring,and insights into N2O production in natural and engineered environments

● 548 representative nor genes were collected to create complete phylogenetic trees. ● The distribution of nor and nod genes were detected in 18 different phyla. ● The most conserved amino acids in NOR were located adjacent to the active site. ● nor-universal and Clade-specific primers were designed, suggested, and tested. Nitric oxide reductases (NORs) have a central role in denitrification, detoxification of nitric oxide (NO) in host-pathogen interactions, and NO-mediated cell-cell signaling. In this study, we focus on the phylogeny and detection of qNOR and cNOR genes because of their nucleotide sequence similarity and evolutionary relatedness to cytochrome oxidases, their key role in denitrification, and their abundance in natural, agricultural, and wastewater ecosystems. We also include nitric oxide dismutase (NOD) due to its similarity to qNOR. Using 548 nor sequences from publicly accessible databases and sequenced isolates from N₂O-producing bioreactors, we constructed phylogenetic trees for 289 qnor/nod genes and 259 cnorB genes. These trees contain evidence of horizontal gene transfer and gene duplication, with 13.4% of the sequenced strains containing two or more nor genes. By aligning amino acid sequences for qnor + cnor, qnor, and cnor, we identified four highly conserved regions for NOR and NOD, including two highly conserved histidine residues at the active site for qNOR and cNOR. Extending this approach, we identified conserved sequences for: 1) all nor (nor-universal); 2) all qnor (qnor-universal) and all cnor (cnor-universal); 3) qnor of Comamonadaceae; 4) Clade-specific sequences; and 5) nod of Candidatus Methylomirabilis oxyfera. Examples of primer performance were confirmed experimentally.     

上软下硬地层深基坑结构变形监测及分析*

为探究在上软下硬地层中进行深基坑开挖时围护结构水平位移与内支撑轴力的变化规律,以广州地区某上软下硬地层盾构井深基坑开挖项目为依托,基于现场监测数据进行分析并运用MIDAS/GTS软件开展深基坑开挖全过程的有限元模拟。将围护结构水平位移模拟值与监测值进行对比,验证模型的准确性;改变围护结构嵌固深度、主体结构厚度等工况,研究上述因素对结构水平位移变化产生的影响。研究结果表明:实测围护结构最大水平位移值11.78 mm,位于长边0.7倍基坑深度附近,坑角处位移值最小;改变结构嵌固深度对坑深15 m以下围护结构位移值影响较大,本工程最佳嵌固深度为1.5~3 m;围护结构水平位移会随着结构主体厚度的增加而减小,但最大位移间差值逐渐减小,结构主体厚度设计值宜为0.8~1 m。     

南水北调大型渡槽结构抗震安全性研究

阐述了南水北调中大型渡槽的抗震问题,分别介绍了基于常微分方程求解器(ODE)和有限元方法的大型渡槽动力计算模型、动力特性分析和设置铅芯橡胶支座(LRB)的隔震分析。研究表明,基于ODE求解器的解析和半解析方法有很好的精度和可靠性,可用于大型渡槽的初步设计。结合所得的研究成果,对南水北调的渡槽抗震提出了合理化建议。     

一种新型废旧轮胎组合拦石结构的试验研究

提出了一种由废旧轮胎组成的拦石结构,该结构用钢丝绳将废旧轮胎进行合理的绑扎,使轮胎与轮胎之间紧密连接,然后将该结构绑扎在用废旧钢轨或钢筋混凝土制作而成的柱子上面.当拦石结构受到落石冲击时,利用废旧轮胎的弹塑性变形吸收冲击能量.为了考察这种由废旧轮胎组成的拦石结构的防护效果,设计了试验模型,采用20 kg的砝码模拟落石,...     

Linking trophic positions and flow structure constraints in ecological networks: Energy transfer efficiency or topology effect?

In the present work we investigate whether the distribution of energy flows in ecosystems responds to criteria of trophic organization. We analyzed weighted and unweighted food webs estimating, for each node, trophic position (TP), Shannon's index of inflow diversity (H) and individual contribution to the whole average mutual information (AMI). Finally, we performed the same analysis on simulated webs that were constructed using the following criteria: (a) preserving topology and varying link strength; (b) modifying position of links and their intensities.     

Invasive species impacts on ecosystem structure and function: A comparison of Oneida Lake, New York, USA, before and after zebra mussel invasion

Exotic species invasion is widely considered to affect ecosystem structure and function. Yet, few contemporary approaches can assess the effects of exotic species invasion at such an inclusive level. Our research presents one of the first attempts to examine the effects of an exotic species at the ecosystem level in a quantifiable manner. We used ecological network analysis (ENA) and a social network analysis (SNA) method called cohesion analysis to examine the effect of zebra mussel (Dreissena polymorpha) invasion on the Oneida Lake, New York, USA, food web. We used ENA to quantify ecosystem function through an analysis of food web carbon transfer that explicitly incorporated flow over all food web paths (direct and indirect). The cohesion analysis assessed ecosystem structure through an organization of food web members into subgroups of strongly interacting predators and prey. Our analysis detected effects of zebra mussel invasion throughout the entire Oneida Lake food web, including changes in trophic flow efficiency (i.e., carbon flow among trophic levels) and alterations of food web organization (i.e., paths of carbon flow) and ecosystem activity (i.e., total carbon flow). ENA indicated that zebra mussels altered food web function by shunting carbon from pelagic to benthic pathways, increasing dissipative flow loss, and decreasing ecosystem activity. SNA revealed the strength of zebra mussel perturbation as evidenced by a reorganization of food web subgroup structure, with a decrease in importance of pelagic pathways, a concomitant rise of benthic pathways, and a reorganization of interactions between top predator fish. Together, these analyses allowed for a holistic understanding of the effects of zebra mussel invasion on the Oneida Lake food web.     

Influence of Landscape Elements in Riparian Buffers on the Conservation of Semiaquatic Amphibians

Abstract:  Studies on riparian buffers have usually focused on the amount of land needed as habitat for the terrestrial life stages of semiaquatic species. Nevertheless, the landscape surrounding wetlands is also important for other key processes, such as dispersal and the dynamics of metapopulations. Multiple elements that influence these processes should therefore be considered in the delineation of buffers. We analyzed landscape elements (forest cover, density of roads, and hydrographic network) in concentric buffers to evaluate the scale at which they influence stream amphibians in 77 distinct landscapes. To evaluate whether our results could be generalized to other contexts, we determined whether they were consistent across the study areas. Amphibians required buffers of 100–400 m of suitable terrestrial habitat, but interspecific differences in the amount of habitat were large. The presence of amphibians was related to roads and the hydrographic network at larger spatial scales (300–1500 m), which suggests that wider buffers are needed with these elements. This pattern probably arose because these elements influence dispersal and metapopulation persistence, processes that occur at large spatial scales. Furthermore, in some cases, analyses performed on different sets of landscapes provided different results, which suggests caution should be used when conservation recommendations are applied to disparate areas. Establishment of riparian buffers should not be focused only on riparian habitat, but should take a landscape perspective because semiaquatic species use multiple elements for different functions. This approach can be complex because different landscape elements require different spatial extents. Nevertheless, a shift of attention toward the management of different elements at multiple spatial scales is necessary for the long-term persistence of populations.     

Spatially explicit modeling of overstory manipulations in young forests: Effects on stand structure and light

Young forests can be manipulated in diverse ways to enhance their ecological values. We used stem maps from two dense, second-growth stands in western Washington and a spatially explicit light model (tRAYci) to simulate effects of five silvicultural manipulations on diameter distribution, species composition, spatial patterning, and light availability. Each treatment removed 30% of the basal area, but differed in how trees were selected for removal. Three primary treatments were thin from below (removing the smallest trees), random thin (removing trees randomly), and gap creation (removing all trees in circles ∼1 tree height in diameter). Two additional treatments combined elements of these approaches: random ecological thin (a mixture of thin from below and random thin) and structured ecological thin (a mixture of thin from below and gap creation).     

Decadal changes in a NW Mediterranean Sea food web in relation to fishing exploitation

We analysed changes in the ecological roles of species, trophic structure and ecosystem functioning using four standardized mass-balance models of the South Catalan Sea (North-western Mediterranean). Models represented the ecosystem during the late 1970s, mid 1990s, early 2000s, and a simulated no-fishing scenario. The underlying hypothesis was that ecosystem models should quantitatively capture the increasing exploitation in the ecosystem from the 1970s to 2000s, as well as differences between the exploited and non-exploited scenarios. Biomass showed a general decrease, while there was an increase in biomass at lower trophic levels (TL) from the 1970s to 2000s. The efficiency of energy transfer (TE) from lower to higher TLs significantly increased with time. The ecosystem during the 1990s showed higher biomass and flows than during the 1970s and 2000s due to an increase in small pelagic fish biomass (especially sardines). Exploited food webs also showed similarities in terms of general structure and functioning due to high intensity of fishing already in the 1970s. This intensity was highlighted with low trophic levels in the catch, high consumption of production by fisheries, medium to high primary production required to sustain the catches and high losses in secondary production due to fishing. Significant differences on ecosystem structure and functioning were highlighted between the exploited and no-fishing scenarios. Biomass of higher TLs increased under the no-fishing scenario and the mean trophic level of the community and the fish/invertebrate biomass ratios were substantially lower in exploited food webs. The efficiency of energy transfer (TE) from lower to higher TLs was lower under the no-fishing scenario, and it showed a continuous decrease with increasing TL. Marine mammals, large hake, anglerfish and large pelagic fish were identified as keystone species of the ecosystem when there was no fishing, while their ecological importance notably decreased under the exploited periods. On the contrary, the importance of small-sized organisms such as benthic invertebrates and small pelagic fish was higher in exploited food webs.     

Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

Four typical coastal sites (rocky shore, sandy shore, mud flat shore, and artificial harbor) at the Yellow Sea were chosen to investigate the spatial and seasonal variations in bacterial communities. This was accomplished by using terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR amplified 16S rDNA fragments. Two kinds of tetrameric restriction enzymes, HhaI and MspI, were used in the experiment to depict the bacterial community diversity in different marine environments. It was found that the community compositions digested by the two enzymes separately were different. However, the results of bacterial community diversity derived from them were similar. The MDA analysis results of T-RFLP profiles coming from HhaI and MspI both exhibited a significant seasonal community shift for bacteria and a relatively low spatial variation among the four locations. With HhaI as the sample, the pair wise T-tests also revealed that variations were minor between each pair of marine environments, with R ranging from 0.198 to 0.349. However, the bacterial community structure in the mud flat site depicted a larger difference than each of the other three sites (R ranging from 0.282 to 0.349).