Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus

Prochlorococcus is both the smallest and numerically most abundant photosynthesizing organism on the planet. While thriving in the warm oligotrophic gyres, Prochlorococcus concentrations drop rapidly in higher-latitude regions. Transect data from the North Pacific show the collapse occurring at a wide range of temperatures and latitudes (temperature is often hypothesized to cause this shift), suggesting an ecological mechanism may be at play. An often used size-based theory of phytoplankton community structure that has been incorporated into computational models correctly predicts the dominance of Prochlorococcus in the gyres, and the relative dominance of larger cells at high latitudes. However, both theory and computational models fail to explain the poleward collapse. When heterotrophic bacteria and predators that prey nonspecifically on both Prochlorococcus and bacteria are included in the theoretical framework, the collapse of Prochlorococcus occurs with increasing nutrient supplies. The poleward collapse of Prochlorococcus populations then naturally emerges when this mechanism of “shared predation” is implemented in a complex global ecosystem model. Additionally, the theory correctly predicts trends in both the abundance and mean size of the heterotrophic bacteria. These results suggest that ecological controls need to be considered to understand the biogeography of Prochlorococcus and predict its changes under future ocean conditions. Indirect interactions within a microbial network can be essential in setting community structure.

Stability criteria for the consumption and exchange of essential resources

Models of pairwise interactions have informed our understanding of when ecological communities will have stable equilibria. However, these models do not explicitly include the effect of the resource environment, which has the potential to refine or modify our understanding of when a group of interacting species will coexist. Recent consumer-resource models incorporating the exchange of resources alongside competition exemplify this: such models can lead to either stable or unstable equilibria, depending on the resource supply. On the other hand, these recent models focus on a simplified version of microbial metabolism where the depletion of resources always leads to consumer growth. Here, we model an arbitrarily large system of consumers governed by Liebig's law, where species require and deplete multiple resources, but each consumer's growth rate is only limited by a single one of these multiple resources. Consumed resources that do not lead to growth are leaked back into the environment, thereby tying the mismatch between depletion and growth to cross-feeding. For this set of dynamics, we show that feasible equilibria can be either stable or unstable, once again depending on the resource environment. We identify special consumption and production networks which protect the community from instability when resources are scarce. Using simulations, we demonstrate that the qualitative stability patterns we derive analytically apply to a broader class of network structures and resource inflow profiles, including cases in which species coexist on only one externally supplied resource. Our stability criteria bear some resemblance to classic stability results for pairwise interactions, but also demonstrate how environmental context can shape coexistence patterns when ecological mechanism is modeled directly.

CRISPRs are associated with bacterial expansion in the human gut during the first year of life

The dynamics of the gut microbiome in infancy have a profound impact on health in adulthood, but the ecological mechanism underlying the dynamics between bacteria and bacteriophages remains poorly understood. CRISPR is a bacterial adaptive immune system to resist bacteriophages; however, the role they play in the dynamics in infants’ gut microbiota is unknown. In this work, using large-scale metagenomic sequencing data from 82 Sweden infants’ gut microbiomes, 1882 candidate CRISPRs were identified and their dynamics were analyzed. The results showed CRISPRs were distributed in dominant bacteria and could target distinct bacteriophages at different time points with largely alternated spacers. In the putative identical CRISPRs, we found the CRISPRs could acquire new spacers and loss old spacers during the first year. In addition, it is the first time to report that gender was a major factor to determine the bacterial richness and the number of CRISPRs and host range of bacteriophages was narrow in silico. Therefore, we concluded that CRISPRs were associated with bacterial expansion. This work improves the understanding of the ecological mechanism behind dynamics in the early life of the human gut and substantially expands the repertoire of predicted CRISPRs providing a resource to study the function of bacterial unknown genes and to enhance the performance of these beneficial bacteria by CRISPR gene-editing technology.

Comparison of Diazotrophic Composition and Distribution in the South China Sea and the Western Pacific Ocean

The variation of diazotrophs has been elusive in multiple SCS and WPO regions due to insufficient data. Therefore, the dynamics of diazotrophic composition and distribution were investigated in this study, based on high-throughput sequencing and quantitative PCR of the nifH gene. We found that Proteobacteria dominated the diazotrophic community in the river-impacted SCS and cyanobacteria and Proteobacteria were more abundant in the ocean-dominated SCS and WPO. The qPCR analysis showed that cyanobacterial Trichodesmium was abundant in the Pearl River plume and in the SCS basin influenced by the Kuroshio intrusion, and it also thrived in the subequatorial region of the WPO. Unicellular cyanobacteria UCYN-A were mainly detected in the river-impacted area, UCYN-B was abundant in the WPO, UCYN-C had a relatively high abundance in the ocean-dominated area, and a preponderance of γ-Proteobacteria γ-24774A11 was observed in the ocean-dominated SCS and pelagic WPO. Diazotrophic communities had significant distance–decay relationships, reflecting clear biogeographic patterns in the study area. The variations of diazotrophic community structure were well explained by dissolved inorganic nitrogen, dissolved inorganic phosphate by an eigenvector spatial variable PCNM1. These results provide further information to help determine the ecological mechanism of elusive diazotrophic communities in different ocean ecosystems.

Changxun Fang. Pioneers of Allelopathy: Wenxiong Lin

Wenxiong Lin did research for > 30 years in plant molecular ecology and agro-ecology, rice allelopathy and continuous monoculture problems/soil sickness of Chinese medicinal plants. His 20 Patents and most publications (about 100) have focussed on (i). Gene regulation of allelochemicals biosynthesis in allelopathic rice, (ii). allelopathic inhibitory effects on weeds, (iii). continuous monoculture problems/soil sickness in medicinal plants and (iv). the influence of allelochemicals and monoculture practice on the rhizospheric micro-environment. He helped in development of microbial fertilizer to alleviate the autotoxicity problem in continuous cropping of Radix pseudostellariae and Rehmannia glutinosa, etc. He had been the President of Asian Allelopathy Society, and got the outstanding achievement from the platform of International Allelopathy Foundation. His student, Dr. Changxun Fang got Rice Award and Grodzinsky Award respectively in the 6th and 8th World Congress of International Allelopathy Society. His elucidation of the molecular ecological mechanism of rice allelopathy was awarded the II Class Prize of Fujian Provincial Scientific and Technological Progress Award in 2007. His researches to find the mechanism of development of continuous cropping obstacle/soil sickness in R. pseudostellariae and its remedy was awarded the I Class Prize of Fujian Provincial Scientific and Technological Progress Award in 2020.

Combined Effects of Microplastics and Biochar on the Removal of Polycyclic Aromatic Hydrocarbons and Phthalate Esters and Its Potential Microbial Ecological Mechanism

Microplastics (MPs) have been attracting wide attention. Biochar (BC) application could improve the soil quality in the contaminated soil. Currently, most studies focused on the effect of MPs or BC on the soil properties and microbial community, while they neglected the combined effects. This study investigated the combined effects of BC or ball-milled BC (BM) and polyethylene plastic fragments (PEPFs) and degradable plastic fragments (DPFs) on the removal of polycyclic aromatic hydrocarbons (PAHs) and phthalate esters (PAEs) from the PAH-contaminated soil and the potential microbial ecological mechanisms. The results showed that BC or BM combined with PEPF could accelerate the removal of PAHs and PAEs. PEPF combined with BM had the most significant effect on the removal of PAHs. Our results indicating two potential possible reasons contribute to increasing the removal of organic pollutants: (1) the high sorption rate on the PEPF and BC and (2) the increased PAH-degrader or PAE-degrader abundance for the removal of organic pollutants.

Microbe-dependent heterosis in maize

ABSTRACTHybrids account for nearly all commercially planted varieties of maize and many other crop plants, because crosses between inbred lines of these species produce F1 offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research (1). The leading hypotheses—which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)—have been able to explain some but not all of the observed patterns of heterosis (2, 3). However, possible ecological drivers of heterosis have largely been ignored. Here we show that heterosis of root biomass and germination in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions, but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved vs. live soil slurries in a growth chamber, and for plants grown in fumigated vs. untreated soil in the field. Together, our results demonstrate a novel, ecological mechanism for heterosis whereby soil microbes generally impair the germination and early growth of inbred but not hybrid maize.