The role of biogeography in shaping diversity of the intestinal microbiota in house mice

The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology. However, little is known regarding the forces shaping variation in these communities and their influence on host fitness. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across Western Europe using pyrosequencing of the bacterial 16S rRNA gene. The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)‐associated communities display properties distinct from those of the lumen, both the caecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the caecal content and mucosa‐associated communities of wild house mice. Overall, we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host.     

高寒草甸植物物种丧失对草原毛虫的影响

植物多样性是调控食物网结构和生态系统功能最重要的生物因素, 植物多样性丧失深刻影响食草动物, 但由于小型食草动物种群数量波动明显、统计随机性较大等困难, 我们对植物多样性丧失如何影响小型食草动物依然知之甚少。基于在青藏高原高寒草甸设置的长期植物物种剔除试验, 本研究于2016-2020年7-8月连续调查了植物物种剔除各处理中草原毛虫(Gynaephora alpherakiif)的数量, 分析了植物物种及功能群丧失对草原毛虫的影响。结果表明, 虽然时空差异及统计随机性是影响草原毛虫数量变化的主要因素, 但植物物种剔除介导的群落差异对草原毛虫数量的影响依然显著: (1)在各观测时段, 优势种线叶嵩草(Kobresia capillifolia)的丧失导致群落中草原毛虫数量显著减少; 禾草类物种丧失也会减少草原毛虫数量, 但其影响仅在8月显著; (2)杂类草物种丧失通过增加群落中禾草物种多度, 可增加草原毛虫数量; 豆科物种丧失使莎草增多, 也会增加草原毛虫数量; (3)各植物功能群部分物种剔除并未显著影响草原毛虫数量。本研究证实了高寒草甸中草原毛虫数量会因优势植物嵩草和禾草的多度减少或禾草物种丧失而显著减少, 但群落总生物量、个体数和物种丰富度、豆科多度以及各功能群植物同比减少, 都对草原毛虫数量没有明显影响。这些结果说明在随机作用主导下, 植物群落中的特定功能群相对多度(而非物种多样性)变化深刻影响草原毛虫适合度, 进而影响生态系功能及服务; 未来生物多样性研究及草地虫害生物防控中应更多考虑统计随机性及植物功能多样性对小型食草动物的影响。     

Phylogenetic dimension of tree communities reveals high conservation value of disturbed tropical rain forests

Aim

The conversion of old‐growth tropical forests into human‐modified landscapes threatens biodiversity worldwide, but its impact on the phylogenetic dimension of remaining communities is still poorly known. Negative and neutral responses of tree phylogenetic diversity to land use change have been reported at local and landscape scales. Here, we hypothesized that such variable responses to disturbance depend on the regional context, being stronger in more degraded rain forest regions with a longer history of land use.

Location

Six regions in Mexico and Brazil.

Methods

We used a large vegetation database (6,923 trees from 686 species) recorded in 98 50‐ha landscapes distributed across two Brazilian and four Mexican regions, which exhibit different degrees of disturbance. In each region, we assessed whether phylogenetic alpha and beta diversities were related to landscape‐scale forest loss, the percentage of shade‐intolerant species (a proxy of local disturbance) and/or the relatedness of decreasing (losers) and increasing (winners) taxa.

Results

Contrary to our expectations, the percentage of forest cover and shade‐intolerant species were weakly related to phylogenetic alpha and beta diversities in all but one region. Loser species were generally as dispersed across the phylogeny as winner species, allowing more degraded, deforested and species‐poorer forests to sustain relatively high levels of evolutionary (phylogenetic) diversity.

Main conclusion

Our findings support previous evidence indicating that traits related to high susceptibility to forest disturbances are convergent or have low phylogenetic signal. More importantly, they reveal that the evolutionary value of disturbed forests is (at least in a phylogenetic sense) much greater than previously thought.

     

Structural basis of pyrrole polymerization in human porphobilinogen deaminase

Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.     

盐池荒漠草地拟步甲昆虫群落时间结构和动态

从2009年3月到10月采用巴氏罐诱导法调查了宁夏盐池四墩子6个不同生境中的拟步甲的群落组成以及时间动态,结果表明,本次调查共采集拟步甲昆虫5431只,计10属20种,个体数最多的是弯齿琵甲Blapsfemoralis femoralis Fischer-Waldheim和克小鳖甲Microdera kraatzi kraatzi Reitter,分别占总数的47.30%和40.66%,不同季节的优势种类不同。从时间动态上看,拟步甲物种数和个体数成显著正相关(r=0.887,P=0.003),表现为5月和7—8月2个发生高峰期,且5月最高。从整个景观来看,优势种克小鳖甲的盛发期在5月和7月,弯齿琵甲的盛发期在5月和8月,不同景观样地略有差异。物种-时间对应分析表明,拟步甲成虫发生可以分为春季发生型、春夏发生型、夏季发生型、夏秋发生型和全年发生型5类。5月拟步甲群落多样性和丰富度最高,不同月的拟步甲群落相似性可以聚为3类,由于植被类型和干扰程度的差异,月间拟步甲群落相似性会有所差异。     

Using space‐for‐time substitution and time sequence approaches in invasion ecology

1. Invasion biologists use two main approaches to evaluate the effects of non‐native species (NNS) on diversity of native species (DNS), namely space‐for‐time and time approaches. These approaches have pitfalls related to lack of controls: the former lacks pre‐invasion data, while the latter often lacks data from non‐invaded sites. 2. We propose a framework that combines space‐for‐time and time approaches and which should result in more focused mechanistic hypotheses and experiments to test the causes of invasibility and the effects of NNS on DNS. We illustrate the usefulness of our framework using two case studies: one with the submersed macrophyte, Hydrilla verticillata, in reservoir and the other with the fish, Geophagus proximus, in a large river–floodplain system. 3. Hydrilla verticillata invaded sites with DNS similar to that found in non‐invaded sites, indicating that biotic and/or abiotic factors did not influence invasion success; however, DNS increased over time in invaded sites compared with non‐invaded sites, suggesting that H. verticillata facilitated natives. In contrast, G. proximus invaded sites with higher DNS than non‐invaded sites, suggesting that biotic and/or abiotic factors favouring natives were important for invasion success, but DNS increased in invaded and non‐invaded sites over time, indicating that an independent factor contributed to DNS increases. 4. Conclusions from both studies would have been inaccurate or incomplete if the space‐for‐time and time approaches had not been used in combination as proposed in our framework.     

Effect of the sequences upstream from the ribosome-binding site on the yield of protein from the cloned gene for phage MS2 coat protein

The translational efficiency of the coat protein gene of phage MS2 has been examined in vivo with respect to neighbouring sequences. The cloned MS2 DNA has been gradually shortened starting at the 5' or 3' terminus, and its effect on coat protein synthesis monitored. Removal of the 3'-terminal sequences had little influence. In contrast, the gradual removal of the 5'-terminal region profoundly reduces translation. Long before the ribosomal binding site (RBS) of the coat protein (CP) gene is reached, the yield of CP has dropped by one order of magnitude. Functional half-lives of the various messengers were found not to be significantly different. Available evidence indicates that the secondary structure of the RBS in native and shortened MS2 RNA is identical. We infer that important determinants for ribosome recognition lie 5' to the RBS region of the MS2 RNA coat gene.