Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

The use of next‐generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets.     

Increases in subsistence farming due to land reform have negligible impact on bird communities in Zimbabwe

Habitat alterations resulting from land‐use change are major drivers of global biodiversity losses. In Africa, these threats are especially severe. For instance, demand to convert land into agricultural uses is leading to increasing areas of drylands in southern and central Africa being transformed for agriculture. In Zimbabwe, a land reform programme provided an opportunity to study the biodiversity response to abrupt habitat modification in part of a 91,000 ha dryland area of semi‐natural savannah used since 1930 for low‐level cattle ranching. Small‐scale subsistence farms were created during 2001–2002 in 65,000 ha of this area, with ranching continuing in the remaining unchanged area. We measured the compositions of bird communities in farmed and ranched land over 8 years, commencing one decade after subsistence farms were established. Over the study period, repeated counts were made along the same 45 transects to assess species'' population changes that may have resulted from trait‐filtering responses to habitat disturbance. In 2012, avian species'' richness was substantially higher (+8.8%) in the farmland bird community than in the unmodified ranched area. Temporal trends over the study period showed increased species'' richness in the ranched area (+12.3%) and farmland (+6.8%). There were increased abundances in birds of most sizes, and in all feeding guilds. New species did not add new functional traits, and no species with distinctive traits were lost in either area. As a result, species'' diversity reduced, and functional redundancy increased by 6.8% in ranched land. By 2020, two decades after part of the ranched savannah was converted into farmland, the compositions of the two bird communities had both changed and became more similar. The broadly benign impact on birds of land conversion into subsistence farms is attributed to the relatively low level of agricultural activity in the farmland and the large regional pool of nonspecialist bird species.     

北京市延庆采砂迹地型湿地植被群落分类与演替分析

采用TWISPAN分析方法,对北京市延庆采矿迹地湿地40个样地51种植物进行了分类排序,将群落类型划分为7个类型,即茵陈蒿-狗尾草-黄花蒿群落、野艾蒿-茵陈蒿-尖叶胡枝子-狗尾草群落、野艾蒿-茵陈蒿-狗尾草-野大豆-苣荬菜群落、狗尾草-苍耳-黄香草木犀-虎尾草群落、狼拔草-野艾蒿-旋覆花-大籽蒿-芦苇群落、香蒲-芦苇-茭白-野大豆-鬼针草群落和竹节灯心草-褐穗莎草-稗群落;同时运用双变量主坐标分析(DPCoA)对51种植物进行了排序分析,研究结果显示研究区存在两种演替规律,即由喜湿旱生耐淹水植物演替为喜旱旱生植物和由湿地挺水植物向湿生植物演替两种类型.对于采砂基地型湿地植被恢复不仅恢复土壤营养条件,调控湿地水分条件也是十分关键的.研究结论将为采砂迹地型湿地恢复提供科学支持.