Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self‐organizing map (SOM)

Aims: To determine the origins of DNA sequences isolated from the rumen microbial ecosystem using a self‐organizing map (SOM). Methods and Results: DNA sequences other than 16S small subunit ribosomal RNA (SSU rRNA) gene sequences that were detected from the rumen were analysed by the SOM method reported by Abe et al. [2000, Self‐Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 365, 27–34]. Because query sequences positioned by SOM were scattered on the master drawing of SOM, it was suggested that many DNA sequences isolated from the rumen were collected from a broad range of micro‐organisms. Although the results obtained by SOM were similar to those obtained by the neighbour‐joining (NJ) method, SOM was able to presume the phylotypes of the query sequences without information about the 16S SSU rRNA gene sequences and homology searches, and to reveal existence of novel micro‐organisms deduced to be cellulolytic bacteria, archaea and methanotrophic bacterium. Conclusions: As the SOM method defined phylotypes of unreported rumen micro‐organisms, it is presumed that these phylotypes would be involved in rumen fermentation in cooperation with known rumen micro‐organisms. Moreover, it is demonstrated that SOM is a useful tool for affiliating DNA sequences, which have no matches in databases. Significance and Impact of Study: Through SOM analysis, a better means of identifying rumen micro‐organisms and estimating their roles in rumen function was provided.     

Development of region-specific emission factors and estimation of methane emission from rice fields in the East, Southeast and South Asian countries

Rice cultivation areas in East, Southeast and South Asia account for 89% of the world total, and field measurements of methane (CH₄) emission from rice cultivation have been widely performed in this area. In this paper, we assembled most of the measurements and developed region‐specific CH₄ emission factors. Efforts were made in order to regionalize rice fields by climate and soil properties, and to incorporate the effect of organic input and water regime on emission. Data on rice cultivation areas of 1995 were collected at subdivision level (province, state, prefecture, etc.). Total emission from these areas was estimated at 25.1 Tg CH₄ year ^{? 1}, of which 7.67 Tg was emitted from China and 5.88 Tg from India. Irrigated and rainfed rice fields contributed 70.4 and 27.5% to the total emission, respectively. Deepwater rice fields had a very small share. A high‐resolution and quality emission distribution map was constructed as the emission was directly estimated at province level and below that, a 30‐second land‐use dataset was used in order to translate the emission to grid format. As the rice cultivation area in the study region accounts for 89% of the world total, extrapolating the estimate to the global scale indicates a global emission of 28.2 Tg CH₄ year ^{? 1}. The estimate was compared with country reports made by local scientists. For some countries – such as Indonesia, Myanmar, Thailand, Vietnam, Japan, South Korea, Pakistan and the Philippines – the results of this estimate agree reasonably well with their country reports (CV < 15%). For some other countries – such as China, India and Bangladesh – there is relatively large disagreement between our estimate and their country reports. The reasons for the discrepancies were discussed.     

Interpreting the SDS-PAGE protein patterns with self-organizing maps: application for the characterization of mosquito-pathogenic Bacillus strains

Aims: To present the pairwise comparison of potential mosquito‐pathogenic Bacillus strains based on their SDS‐PAGE protein patterns and to evaluate their characteristic toxicity patterns. Methods and Results: In this work, 20 Bacillus strains were subjected to qualitative toxicity tests against Aedes aegypti and Culex quinquefasciatus larvae. The selected strains were then characterized by SDS‐PAGE protein profiles. The highly heterogeneous multiple protein components of protein patterns were analysed using self‐organizing map (SOM), a ‘visualization and clustering’ tool. Members of mosquitocidal Bacillus species were classified in four distinct clusters, and then toxicity patterns were examined. Cluster (1, 1) comprised of three highly toxic strains of Bacillus sphaericus: SPH88, 1593 and KSD‐4; cluster (1, 2) consisted of two B. sphaericus strains: SSII‐1 and Bsp‐R that showed weak larvicidal activity; cluster (2, 1) constituted two B. sphaericus strains: WHO2297 and ISPC‐5 that possessed moderate toxicity; and cluster (2, 2) contained four B. thuringiensis ssp. israelensis strains: ONR‐60A, HD500, IPS70 and IPS82 belonging to serotype H14 but exhibited moderate to high mosquito larvicidal toxicity. Conclusions: SOM served as a colour‐coded alternate for easy visualization of similarities or dissimilarities between the strains even at the infra subspecies level. Furthermore, characteristic toxicity patterns of Bacillus strains of different clusters were determined. Significance and Impact of the Study: Analysis of electrophoretic protein patterns using SOM provides a better insight into the inter‐relationships of bacterial strains through similarity‐based clustering and pairwise comparison of two strains.     

The geographical distribution of Naididae (Oligochaeta) in Britain

A compilation of records of the geographical location of naidid species in Britain is presented. Many species previously considered rare are shown to be widely distributed.     

Genetic diversity of Ligula intestinalis (Cestoda: Diphyllobothriidea) based on analysis of inter‐simple sequence repeat markers

In order to investigate the genetic diversity of Ligula intestinalis populations, nine inter‐simple sequence repeat (ISSR) markers were applied to populations from nine geographical areas around the world and 10 host species. The 110 loci selected from the ISSR patterns produced revealed high variability among the analysed samples, with a polymorphism of 100% and a global coefficient of gene differentiation estimated by Nei’s index (G_ST) of 0.776. Major genetic differentiation was found to be correlated to five broad geographical regions (Europe, China, Canada, Australia and Algeria). Nevertheless, no significant genetic variation was found among European isolates, although they originated from disparate geographical localities and/or unrelated hosts. Classical classification methods: maximum parsimony and factorial correspondence analysis were compared with an advanced statistical method: the self‐organizing map (SOM). The results demonstrated that the ISSR approach is rapid and inexpensive and provides reliable markers to assess genetic diversity of L. intestinalis. Furthermore, SOM artificial neuronal networks are considered to provide an efficient alternative tool for mapping the genetic structures of parasite populations.     

Multi-scale analysis of responses of stream macrobenthos to forestry activities and environmental context

1. Forestry activities can greatly modify the structure and function of invertebrate communities in streams, but the ability to detect effects of forestry may depend on the spatial scale considered, the choice of response metric and the environmental context. In this study, a multi‐scale, multi‐metric approach was used to compare the usefulness of proximate and larger‐scale measurements of forestry activity for understanding the impacts of forestry on stream macrobenthos. 2. Site‐specific responses of macrobenthic communities to forestry activities measured at four spatial scales (sub‐basin and 8‐, 2‐ and 0.5‐km radii upstream of study sites) were examined for 90 riffle sites distributed among 22 tributary streams (Strahler order 1–5) of the Cascapedia River basin, Quebec, Canada. 3. Multiple regression models and canonical correspondence analysis were used to relate six biological metrics (taxonomic richness, numerical density, biomass density, normalised biomass spectrum, individual body mass and community structure) to variables quantifying logging 1–19 years prior to the study and road density. Environmental predictors (variables quantifying local habitat or landscape features) were included in all analyses to statistically account for environmental context and increase the likelihood of detecting potentially subtle forestry impacts. 4. Forestry activities measured at the larger (sub‐basin and 8 km) scales were linked to decline in taxonomic richness, increase in numerical and biomass densities and shift in size structure of benthic macroinvertebrates, indicating that analyses encompassing larger areas, up to the full basin, may allow for more sensitive detection of effects than those of more limited span. 5. These responses primarily reflected marked increases in the abundance of chironomids and decline in the number of trichopteran taxa with increasing areal coverage of recent (≤2–4 years) cuts, suggesting that larger, longer‐lived and possibly more specialised taxa were more vulnerable to forestry impacts than smaller, multivoltine, generalist invertebrates. After partialling out the influence of other variables, rapid decline in richness occurred even when <1% of the basin had been clear cut in the year prior to the study. 6. Effects of forestry were detected after statistically accounting for natural environmental variability, which may have otherwise concealed those effects. The combined use of multiple biological metrics, partialling out of environmental effects and measurement of impacts at multiple spatial scales may be a broadly applicable approach for enhancing sensitivity and facilitating interpretation in studies of anthropogenic effects on macroinvertebrate communities.     

北极村国家级自然保护区狍栖息地适宜性及活动节律

掌握野生动物栖息地适宜性及活动节律对科学保护森林生态系统具有重要意义。狍(Capreolus pygargus)作为森林生态系统中重要组成部分,其生物学习性对于植被更新及同域物种分布具有指示作用,掌握其栖息地适宜性及活动节律是恢复生物多样性的基础。于2022年6月-2023年5月在北极村国家级自然保护区采用样线调查和相机监测相结合的方法收集狍活动信息,通过随机布设方法在保护区内共布设35条样线和140台红外相机,并利用最大熵(MaxEnt)栖息地建模及核密度估计法分析狍的栖息地适宜性与活动节律,结果表明:(1) MaxEnt模型的ROC曲线评价结果的平均AUC值为0.839,能够较好的反映研究区域狍栖息地适宜性的实际分布情况;(2)研究利用的14个变量中,距离河流越远出现概率越低是影响狍栖息地选择的关键变量,贡献率达34%。其次针阔混交林、常绿针叶林、林间小路、海拔、草地和居民区是影响狍栖息地质量的次要变量;(3)保护区内狍适宜栖息地和次适宜栖息地面积分别为240.44km²和490.64 km²,占研究区域总面积的17.48%和35.67%,主要分布于保护区中部和东部,西部适宜栖息地面积较少且破碎化较为严重;(4)活动节律分析表明,狍在9:00左右达到日活动高峰;不同季节狍活动节律存在差异,暖季狍活动节律具有晨昏性,冷季狍上午和下午的活动高峰期分别延迟和提前。基于研究结果提出以下保护建议:(1)加大保护区周边人类活动的管控力度,根据不同人为干扰强度针对性地对狍种群进行保护;(2)通过加强栖息地连通性管理、构建栖息地廊道等方法使破碎的栖息地连接成整体,促进保护区狍个体间交流。研究获得的结果为分布于我国最北端狍种群的保护与恢复提供了基础数据,对于推动该地区生物多样性保护具有重要意义。