Heterotrophic Bacteria Play an Important Role in Endemism of Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007, a Full-Year Shooting Woody Bamboo

The previous studies show soil microbes play a key role in the material and nutrient cycles in the forest ecosystem, but little is known about how soil microbes respond to plant distribution, especially in the soil bacterial community in woody bamboo forests. Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007 is known as the only bamboo species producing shoots all year round in natural conditions. Endemic to the Dawei mountain in Yunnan of China, this species is a good case to study how soil bacteria respond to plant endemic distribution. In this work, we assayed the soil chemical properties, enzyme activity, changes in the bacterial community along the distribution range of the C. pingbianense forest. The results showed that soil nutrients at the range edge were nitrogen-rich but phosphorus-deficient, and soil pH value and soil urease activity were significantly lower than that of the central range. No significant difference was detected in soil bacterial diversity, community composition, and function between the central and marginal range of C. pingbianense forest. Notably, the relative abundance of heterotrophy bacteria, such as Variibacter and Acidothermus, in the soil of the C. pingbianense forest was significantly higher than that of the outside range, which may lead to a higher soil organic carbon mineralization rate. These results imply that abundant heterotrophy bacteria were linked to the endemism and full-year shooting in C. pingbianense. Our study is amongst the first cases demonstrating the important role of heterotrophy bacteria in the distribution formation of endemic woody bamboos in special soil habitats, and provides insight into germplasm conservation and forest management in woody bamboos.

Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics

Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes, than with “narrow” functions specialized by specific microorganisms. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with “broad” and “narrow” functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five “broad” and the five “narrow” functions that we chose. Our results revealed that compared with the five “broad” functions, soil microbes capable of performing the five “narrow” functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in “narrow” functions. Co-occurrence networks indicated that microorganisms conducting “broad” functions were positively related, but microbes specializing “narrow” functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between “broad” and “narrow” functions in soil microbes, as the association of functional diversity with taxonomy were greater in the five “narrow” rather than the five “broad” functions.

Characterization of opposing responses to phenol by Bacillus subtilis chemoreceptors

Bacillus subtilis employs ten chemoreceptors to move in response to chemicals in its environment. While the sensing mechanisms have been determined for many attractants, little is known about the sensing mechanisms for repellents. In this work, we investigated phenol chemotaxis in B. subtilis . Phenol is an attractant at low, micromolar concentrations, and a repellent at high, millimolar concentrations. McpA was found to be the principal chemoreceptor governing the repellent response to phenol and other related aromatic compounds. In addition, the chemoreceptors McpC and HemAT were found to govern the attractant response to phenol and related compounds. Using chemoreceptor chimeras, McpA was found to sense phenol using its signaling domain rather than its sensing domain. These observations were substantiated in vitro, where direct binding of phenol to the signaling domain of McpA was observed using saturation-transfer difference nuclear magnetic resonance. These results further advance our understanding of B. subtilis chemotaxis and further demonstrate that the signaling domain of B. subtilis chemoreceptors can directly sense chemoeffectors. IMPORTANCE Bacterial chemotaxis is commonly thought to employ a sensing mechanism involving the extracellular sensing domain of chemoreceptors. Some ligands, however, appear to be sensed by the signaling domain. Phenolic compounds, commonly found in soil and root exudates, provide environmental cues for soil microbes like Bacillus subtilis . We show that phenol is sensed both as an attractant and a repellent. While the mechanism for sensing phenol as an attractant is still unknown, we found that phenol is sensed as a repellent by the signaling domain of the chemoreceptor McpA. This study furthers our understanding of the unconventional sensing mechanisms employed by the B. subtilis chemotaxis pathway.

Effects of Different Soils on the Biomass and Photosynthesis of Rumex nepalensis in Subalpine Region of Southwestern China

The performance of Rumex nepalensis, an important medicinal herb, varies significantly among subalpine grasslands, shrublands and forest ecosystems in southwestern China. Plant–soil feedback is receiving increasing interest as an important driver influencing plant growth and population dynamics. However, the feedback effects of soils from different ecosystems on R. nepalensis remain poorly understood. A greenhouse experiment was carried out to identify the effects of different soil sources on the photosynthesis and biomass of R. nepalensis. R. nepalensis was grown in soils collected from the rooting zones of R. nepalensis (a grassland soil, RS treatment), Hippophae rhamnoides (a shrub soil, HS treatment), and Picea asperata (a forest soil, PS treatment). The chlorophyll contents, net photosynthetic rates, and biomasses of R. nepalensis differed significantly among the three soils and followed the order of RS > HS > PS. After soil sterilization, these plant parameters followed the order of RS > PS > HS. The total biomass was 16.5 times higher in sterilized PS than in unsterilized PS, indicating that the existence of soil microbes in P. asperata forest ecosystems could strongly inhibit R. nepalensis growth. The root to shoot biomass ratio of R. nepalensis was the highest in the sterilized PS but the lowest in the unsterilized PS, which showed that soil microbes in PS could change the biomass allocation. Constrained redundancy analysis and path analysis suggested that soil microbes could impact the growth of R. nepalensis via the activities of soil extracellular enzymes (e.g., β-1,4-N-acetylglucosaminidase (NAG)) in live soils. The soil total soluble nitrogen concentration might be the main soil factor regulating R. nepalensis performance in sterilized soils. Our findings underline the importance of the soil microbes and nitrogen to R. nepalensis performance in natural ecosystems and will help to better predict plant population dynamics.

Soil Microbes Alter the Diversity-Invasibility Relationship by Promoting a Complementarity Effect on Community Invasion Resistance

Background Soil microbes can affect both the invasiveness of exotic plants and the invasibility of native plant communities, but it still remains unclear whether soil microbes can influence the relationship between native plant diversity and community invasibility.Methods We constructed native plant communities with three levels of species richness (one, three, or six species) in unsterilized or sterilized soil (i.e., with or without soil microbes) and either prevented their invasion by exotic plants or allowed them to be invaded by each of three exotic species (Solidago canadensis, Erigeron canadensis or Symphyotrichum subulatum), which are highly invasive in China. The soils conditioned by the native plant communities that were not invaded by the exotic species were used as soil microbe inocula to test whether species richness-induced differences in soil microbes affected the growth of each of the three invasive species.Results Compared with soils containing microbes, the absence of soil microbes weakened the negative species richness-invasibility relationship, indicating that soil microbes can contribute to higher invasion resistance in more diverse native plant communities. In the presence of soil microbes, the higher invasion resistance of more diverse communities was mainly ascribed to the complementarity effect. However, soil microbes from communities with a higher species richness did not have a stronger negative effect on the growth of any of the three invasive species. Conclusion Soil microbes can alter the diversity-invasibility relationship by promoting the complementarity effect on community invasion resistance. Our results highlight the importance of integrating the role of soil microbes when testing the diversity-invasibility hypothesis.

Making protons tag along with electrons

Every living cell needs to get rid of leftover electrons when metabolism extracts energy through the oxidation of nutrients. Common soil microbes such as Geobacter sulfurreducens live in harsh environments that do not afford the luxury of soluble, ingestible electron acceptors like oxygen. Instead of resorting to fermentation, which requires the export of reduced compounds (e.g. ethanol or lactate derived from pyruvate) from the cell, these organisms have evolved a means to anaerobically respire by using nanowires to export electrons to extracellular acceptors in a process called extracellular electron transfer (EET) [ 1]. Since 2005, these nanowires were thought to be pili filaments [ 2]. But recent studies have revealed that nanowires are composed of multiheme cytochromes OmcS [ 3, 4] and OmcZ [ 5] whereas pili remain inside the cell during EET and are required for the secretion of nanowires [ 6]. However, how electrons are passed to these nanowires remains a mystery ( Figure 1A). Periplasmic cytochromes (Ppc) called PpcA-E could be doing the job, but only two of them (PpcA and PpcD) can couple electron/proton transfer — a necessary condition for energy generation. In a recent study, Salgueiro and co-workers selectively replaced an aromatic with an aliphatic residue to couple electron/proton transfer in PpcB and PpcE (Biochem. J. 2021, 478 (14): 2871–2887). This significant in vitro success of their protein engineering strategy may enable the optimization of bioenergetic machinery for bioenergy, biofuels, and bioelectronics applications.