互惠共生微生物：新资源，新技术，新机遇，新挑战

2020年9月联合国环境规划署发布《全球生物多样性展望-5》(GBO-5)报告,助力世界实现协商一致的愿景——到2050年“与自然和谐相处”。其实,原本地球上的所有生物都是相互依存、互惠共生于地球村的,尽管存在少数“坏分子”。但由于人类的贪婪,过度扩张才导致地球“千疮百孔”的面貌,严重威胁到人类文明可持续发展。通过最近20年的研究,互惠共生微生物(mutualistic symbiotic microbes,MSM)从其丰富的群落多样性到种质新资源、从多种多样的生理生态功能到作用机制、从基础探究到新技术研发,为实现人与自然和谐相处的愿景提供了新机遇,同时也面临新挑战。令人可喜的是,中国在MSM研究领域取得了令世人瞩目的成果。《微生物学通报》于2020年11期特别推出了“互惠共生微生物专栏”,旨在展现中国MSM研究的最新进展和成果,促进生物共生学的发展壮大。     

互惠共生微生物多样性研究概况

所谓互惠共生微生物(mutualistic symbiotic microbes,MSM)是指能定殖其他生物构建互惠共生体系的微生物,主要包括互惠共生细菌、互惠共生放线菌和互惠共生真菌等.MSM种类繁多、分布广泛、物种多样性丰富,涉及原核生物界和真菌界等.MSM定殖人体、动物、植物、藻类或其他真菌,可构建各自相应的互惠...     

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms

Sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alternative tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomorphic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution.     

Cross-species transfer of nuclear microsatellite markers: potential and limitations

Molecular ecologists increasingly require 'universal' genetic markers that can easily be transferred between species. The distribution of cross-species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross-species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross-species transferable markers.     

Production of recombinant proteins by microbes and higher organisms

Large proteins are usually expressed in a eukaryotic system while smaller ones are expressed in prokaryotic systems. For proteins that require glycosylation, mammalian cells, fungi or the baculovirus system is chosen. The least expensive, easiest and quickest expression of proteins can be carried out in Escherichia coli. However, this bacterium cannot express very large proteins. Also, for S–S rich proteins, and proteins that require post-translational modifications, E. coli is not the system of choice. The two most utilized yeasts are Saccharomyces cerevisiae and Pichia pastoris. Yeasts can produce high yields of proteins at low cost, proteins larger than 50 kD can be produced, signal sequences can be removed, and glycosylation can be carried out. The baculoviral system can carry out more complex post-translational modifications of proteins. The most popular system for producing recombinant mammalian glycosylated proteins is that of mammalian cells. Genetically modified animals secrete recombinant proteins in their milk, blood or urine. Similarly, transgenic plants such as Arabidopsis thaliana and others can generate many recombinant proteins.     

Genetically engineered resistance to bacterial and fungal pathogens

In the past 10 years, different strategies have been used to produce transgenic plants that are less susceptible to diseases caused by phytopathogenic fungi and bacteria. Genes from different organisms, including bacteria, fungi and plants, have been successfully used to develop these strategies. Some strategies have been shown to be effective against different pathogens, whereas others are specific to a single pathogen or even to a single pathovar or race of a given pathogen. In this review, we present the strategies that have been employed to produce transgenic plants less susceptible to bacterial and fungal diseases and which constitute an important area of plant biotechnology.The authors are with the Departamento de Ingeniería Genética de Plantas. Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Km 9.6 del Libramiento Norte carretera Irapuato-León, Apdo Postal 629, Irapuato, Mexico.     

Cascading predation effects of Daphnia and copepods on microbial food web components

1. We performed a mesocosm experiment to investigate the structuring and cascading effects of two predominant crustacean mesozooplankton groups on microbial food web components. The natural summer plankton community of a mesotrophic lake was exposed to density gradients of Daphnia and copepods. Regression analysis was used to reveal top–down impacts of mesozooplankton on protists and bacteria after days 9 and 15. 2. Selective grazing by copepods caused a clear trophic cascade via ciliates to nanoplankton. Medium‐sized (20–40 μm) ciliates (mainly Oligotrichida) were particularly negatively affected by copepods whereas nanociliates (mainly Prostomatida) became more abundant. Phototrophic and heterotrophic nanoflagellates increased significantly with increasing copepod biomass, which we interpret as an indirect response to reduced grazing pressure from the medium‐sized ciliates. 3. In Daphnia‐treatments, ciliates of all size classes as well as nanoflagellates were reduced directly but the overall predation effect became most strongly visible after 15 days at higher Daphnia biomass. 4. The response of bacterioplankton involved only modest changes in bacterial biomass and cell‐size distribution along the zooplankton gradients. Increasing zooplankton biomass resulted either in a reduction (with Daphnia) or in an increase (with copepods) of bacterial biovolume, activity and production. Patterns of bacterial diversity, as measured by polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE), showed no distinct grouping after 9 days, whereas a clear treatment‐coupled similarity clustering occurred after 15 days. 5. The experiment demonstrated that zooplankton‐mediated predatory interactions cascade down to the bacterial level, but also revealed that changes occurred rather slowly in this summer plankton community and were most pronounced with respect to bacterial activity and composition.     

Estimates of protozoan- and viral-mediated mortality of bacterioplankton in Lake Bourget (France)

1. We performed three, 1‐week in situ experiments in March‐April (expt 1), May (expt 2) and August (expt 3) 2003 in order to assess protozoan and virus‐induced mortality of heterotrophic bacteria in a French lake. Viral and bacterial abundances were obtained using flow cytometry (FCM) while protozoa were counted using epifluorescence microscopy (EFM). 2. A dilution approach, applied to pretreated grazer‐free samples, allowed us to estimate that viral lysis could be responsible for 60% (expt 1), 35% (expt 2) and 52% (expt 3) of daily heterotrophic bacterial mortality. Flagellate (both mixotrophic and heterotrophic) grazing in untreated samples, was responsible for 56% (expt 1), 63% (expt 2) and 18% (expt 3) of daily heterotrophic bacteria removal. 3. These results therefore suggest that both viral lysis and flagellate grazing had a strong impact on bacterial mortality, and this impact varied seasonally. 4. From parallel transmission electron microscopy (TEM) analysis, we found that the burst size (i.e. the number of viruses potentially released per lysed cell) ranged from nine to 25 (expt 1), 10 to 35 (expt 2) and eight to 25 (expt 3). The percentage of infected heterotrophic bacteria was 5.7% (expt 1), 3.4% (expt 2) and 5.7% (expt 3) so that the calculated percentage of bacterial mortality induced by viruses was 6.3% (expt 1), 3.7% (expt 2) and 6.3% (expt 3). 5. It is clear that the dilution‐FCM and TEM methods yielded different estimates of viral impact, although both methods revealed an increased impact of viruses during summer.     

How well can the fatty acid content of lake seston be predicted from its taxonomic composition?

1. Results from the few field studies that have tried to relate seston taxonomic and fatty acid (FA) composition suggest that phytoplankton composition only partially explains seston FA composition. However, in these studies, the heterotrophic components of seston (i.e. bacteria and heterotrophic protists) have not been accounted for. 2. The general premise of this article was that including the contribution of heterotrophs to seston biomass can improve understanding of the variability in seston FA composition. This was tested for an oligotrophic clearwater lake, in which the taxonomic and FA compositions of seston, fractionated into three size classes, were monitored every 2 weeks over a growth season. The relationship between seston taxonomic and FA composition was studied using canonical correlation analyses. 3. Because of their relative richness in branched FA and lack of highly unsaturated FAs (HUFA) compared to autotrophs and other protists, the contribution of bacteria to seston biomass was shown to explain an important part of the differences in FA composition between the different seston size classes. Phytoplankton seasonal succession also affected the FA composition of seston but only for size classes that were dominated by autotrophs. 4. The results also indicated that heterotrophic protists such as ciliates and heterotrophic nanoflagellates might substantially influence the seston FA, and especially, HUFA, composition. 5. The per cent of variability in seston FA composition that was explained by its taxonomic composition was still relatively low, even when taking account of heterotrophs. Hence, other possible influences, such as phytoplankton species composition, physiological state and the contribution of terrestrial detritus, need investigation.     

植物物种形成的模式与机制

物种形成是指由已有的物种通过各种进化机制进化出新物种的过程。持续不断的物种形成产生了地球上灿烂的生物物种多样性。然而,研究人员对物种形成的模式与机制的了解却非常有限。一直以来,谱系分裂被认为是最重要的物种形成模式,但在植物中,谱系融合,即通过杂交形成新物种的过程,也是一个非常重要的物种形成模式。经过几十年的研究才逐渐认识到,生殖隔离是差异适应和遗传漂变的副产品,而不是物种形成的前提。相比合子形成后隔离,合子形成前的隔离在物种形成过程中更早地发挥作用。合子形成前的隔离,尤其是生态地理的隔离是植物中最重要的隔离机制。一些基于QTLs分析的研究发现,基因组中的少数主效位点在物种形成中起了关键作用,并且这些位点往往受到自然选择的作用。适应性辐射往往发生在隆起的山脉和新形成的岛屿上,很可能与这些地方能够提供很多可利用的生态位有关。最新的物种形成理论认为,基因是物种形成的基本单位,不同的物种可以在非控制物种差异适应性状的位点上存在基因流。这一观点为植物物种形成的研究提供了新的思路。随着植物物种形成研究的深入,越来越多植物物种形成基因被分离,包括花色素苷合成通路和S-基因座上的一些关键基因,揭示了植物物种形成的分子机制。前期的研究主要集中在模式植物和农作物上,许多生态上非常有趣的非模式植物还未得到广泛的研究。在未来的研究中,还需要更多来自非模式植物的例子以全面理解植物物种形成的多样化机制。