Genotoxicity detected in wild mice living in a highly polluted wetland area in south western Spain

A field study was carried out in the south of the Iberian Peninsula in an industrial area in the neighbourhood of Huelva city, SW Spain, and in a natural area (Do?ana National Park) for comparison, to estimate the genetic risk induced by environmental pollution in wild mice. Genotoxic effects in a sentinel organism, the Algerian mice (Mus spretus) free living in the industrial area were compared with animals of the same species living in the natural protected area. The single cell gel electrophoresis, or Comet assay, was performed as a genotoxicity test in peripheral blood of mice. Our results clearly show that mice free living in the contaminated area bear a high burden of genetic damage as compared with control individuals. The results suggest that the assessing of genotoxicity levels by the Comet assay in wild mice can be used as a valuable test in pollution monitoring and environmental conservation.     

Duetting and mate-guarding in Australian magpie-larks (Grallina cyanoleuca)

A recently favored hypothesis is that duetting in birds has a mate-guarding function: a male responds vocally to his partner’s song, thereby forming a duet that repels males who are attracted to her song. Previous studies have not provided unambiguous tests of the mate-guarding hypothesis because: (1) the probability of a male answering his partner’s song has not been shown to increase specifically when the female is fertile, and (2) the probability of a male answering his partner’s song has not been assessed separately from simply a higher song initiation rate. We investigated extra-pair paternity, mate-guarding, and duetting in the socially monogamous Australian magpie-lark (Grallina cyanoleuca). DNA fingerprinting revealed that 3% of young were the result of extra-pair paternity, and we found that males guarded fertile females by staying close to them. However, males did not initiate songs at a higher rate when females were fertile and actually reduced their probability of replying to female song during this period. We conclude that although male magpie-larks did guard fertile females in an attempt to prevent extra-pair copulations, they did not use duetting for this purpose. Received: 10 May 1999 / Received in revised form: 27 September 1999 / Accepted: 2 October 1999     

Social and mating system of cooperatively breeding laughing kookaburras (Dacelo novaeguineae)

DNA fingerprinting was combined with field observations over four breeding seasons to investigate the social structure and mating system of the laughing kookaburra (Dacelo novaeguineae). Groups comprised a socially dominant pair and up to six helpers of either sex. Helpers were always recruited from young hatched in the group. Territorial inheritance, which is a feature of other cooperative breeders and an oft-cited benefit of philopatry, did not occur. Helpers only attained dominant status in an established group by dispersing into a vacant dominant position in that group. However, helpers could also form new groups by excising a new territory, often through a ”budding” process. The mating system was overwhelmingly monogamous. There were no cases of extra-group parentage in a sample of 140 nestlings; within groups of three or more birds, dominance predicted parentage almost perfectly (99.2% of 129 nestlings), irrespective of whether helpers in the group were related to one or both dominant birds. This is contrary to predictions from models of reproductive skew, possibly because they currently fail to incorporate the willingness of females to share reproduction among males. Received: 15 May 1999 / Received in revised form: 2 November 1999 / Accepted: 6 November 1999     

从顽拗植物荔枝中提取基因组DNA技术的研究

针对荔枝体内含有大量影响ＤＮＡ提取质量的多酚等次生代谢物质的特点,在常规ＳＤＳ和ＣＴＡＢ提取方法的基础上做了技术改进,即在核裂解之间先破碎细胞,将存在于细胞质中次生物质除去后再裂解细胞核,同时加入活性炭以吸咐杂质反复清洗几次后加入核型解液释放基因组ＤＮＡ,纯化之后经外观和电泳检测,以及Ｄ２６０ｎｍ和Ｄ２８０ｎｍ比值的测定,限制性内切酶反应,ＰＣＲ扩增的结果表明,用改进方法提取的ＤＮＡ无论在纯度上还     

DNA同源性分析最终确定新疆中华根瘤菌（Sinorhizobium xinjiangensis）为一独立种

针对S.xinjiangensis分类地位的争议,从新疆再次分离获得34株快生大豆根瘤菌,在16SrDNAPCR-RFLP分析和SDS全细胞蛋白电泳分群的基础上,进行了16SrDNA全序列相似性和DNA同源性分析.所测4个菌株和S.fredii模式菌株USDA205的16SrDNA全序列有很高的相似性.而DNA同源性分析说明新分离的菌株代表与原定的S.xinjiangensis为一个DNA同源群.其模式菌株CCBAU110与S.fredii的2株参比菌株USDA194、2048之间的DNA同源性分别为31.5%和28.7%.S.fredii的模式菌株USDA205与新分离的菌株代表及原定的S.xinjiangensis的模式菌株和2个参比菌株之间的DNA同源性为20.8%～39%,远低于70%.属于种水平上的差异.按照国际细菌分类委员会以DNA同源性≥70%且△Tm≤5℃作为定种的标准,S.xinjiangensis是Sinorhizobium属中不同于S.fredii的一个独立的种.表3参20     

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates, spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish genera previously recorded in the Gulf. Sites of similar habitat type were also similar in eDNA composition. The species accumulation analyses showed that the number of sample replicates was insufficient for some sampling sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate diversity in the study area. Our results confirm that seawater samples contain habitat-characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.     

Backwater Confluences of the Ohio River: Organic and Inorganic Fingerprints Explain Sediment Dynamics in Wetlands and Marinas

In the Ohio River (OR), backwater confluence sedimentation dynamics are understudied, however, these river features are expected to be influential on the system’s ecological and economic function when integrated along the river’s length. In the following paper, we test the efficacy of organic and inorganic tracers for sediment fingerprinting in backwater confluences; we use fingerprinting results to evidence sediment dynamics controlling deposition patterns in confluences used for wetland and marina functions; and we quantify the spatial extent of tributary drainages with wetland and marina features in OR confluences. Both organic and inorganic tracers statistically differentiate sediment from stream and river end‐members. Carbon and nitrogen stable isotopes produce greater uncertainty in fingerprinting results than inorganic elemental tracers. Uncertainty analysis of the nonconservative tracer term in the organic matter fingerprinting application estimates an apparent enrichment of the carbon stable isotopes during instream residence, and the nonconservativeness is quantified with a statistical approach unique to the fingerprinting literature. Wetland and marina features in OR confluences impact 42% and 11% of tributary drainage areas, respectively. Sediment dynamics show wetland and marina confluences experience deposition from river backwaters with longitudinally linear and nonlinear patterns, respectively, from sediment sources.     

浮游动物DNA宏条形码标志基因比较研究

DNA宏条形码技术作为一种新型生物监测方法,在未来生态环境监测中有巨大的应用潜力。目前,浮游动物DNA宏条形码监测仍在发展阶段,需要首先对其(采样方法、引物选择和数据分析等)进行标准化和调整,然后才能用于常规流域生态监测。其中,如何选择合适的PCR扩增引物是DNA宏条形码生物监测标准化的关键问题之一。本研究比较了COI、18SV9和16S通用引物在浮游动物DNA宏条形码监测中的差异,为初步建立规范化的浮游动物DNA宏条形码监测方法提供技术支撑。结果表明,16S引物对浮游动物具有更好的特异性,其产生的操作分类单元(operational taxonomic unit, OTU)有88.1%属于浮游动物。虽然18SV9引物具有更高的物种覆盖度,不仅能扩增出浮游动物,还能扩增出大量藻类和真菌,但其物种识别敏感性较差,不适合浮游动物物种水平多样性监测。COI引物的浮游动物物种特异性、物种覆盖度和物种识别敏感性都适中,检出的浮游动物物种数量高于18SV9引物和16S引物,更加适合浮游动物DNA宏条形码监测。     

Tracing the sources of refractory dissolved organic matter in a large artificial lake using multiple analytical tools

Structural and chemical characteristics of refractory dissolved organic matter (RDOM) from seven different sources (algae, leaf litter, reed, compost, field soil, paddy water, treated sewage) were examined using multiple analytical tools, and they were compared with those of RDOM in a large artificial lake (Lake Paldang, Korea). Treated sewage, paddy water, and field soil were distinguished from the other sources investigated by their relatively low specific UV absorbance (SUVA) values and more pronounced fulvic-like versus humic-like fluorescence of the RDOM samples. Microbial derived RDOM from algae and treated sewage showed relatively low apparent molecular weight and a higher fraction of hydrophilic bases relative to the total hydrophilic fraction. For the biopolymer types, the presence of polyhydroxy aromatics with the high abundance of proteins was observed only for vascular plant-based RDOM (i.e., leaf litter and reed). Molecular weight values exhibited positive correlations with the SUVA and the hydrophobic content among the different RDOM, suggesting that hydrophobic and condensed aromatic structures may be the main components of high molecular weight RDOM. Principal component analysis revealed that approximately 77% of the variance in the RDOM characteristics might be explained by the source difference (i.e., terrestrial and microbial derived) and a tendency of further microbial transformation. Combined results demonstrated that the properties of the lake RDOM were largely affected by the upstream sources of field soil, paddy water, and treated sewage, which are characterized by low molecular weight UV-absorbing and non-aromatic structures with relatively high resistance to further degradation.     

Comparison of an assay for Dehalococcoides DNA and a microcosm study in predicting reductive dechlorination of chlorinated ethenes in the field

The study aims to compare the detection of 16S rRNA gene of Dehalococcoides species and the microcosm study for biotransformation in predicting reductive dechlorination of chlorinated ethenes in ground water at hazardous waste sites. A total of 72 ground water samples were collected from 12 PCE or TCE contaminated sites in the United States. The samples were analyzed and used to construct microcosms in the laboratory. The results showed that the presence of Dehalococcoides DNA was well associated with dechlorination to ethene in the field. Nearly half of the wells where Dehalococcoides DNA was detected had ethene as a dechlorination end product. In comparison, for ground water samples of 16 wells where ethene was detected, ethene was produced in 11 of the corresponding microcosms. For most microcosms, during two years of incubation, dechlorination was less extensive than that observed in the field.