Cover crops are considered an integral component of agroecosystems because of their positive impacts on biotic and abiotic indicators of soil health. At present, we know little about the impact of cover crop types and diversity on the organic carbon (OC) contents of different soil aggregate-size classes. In this study, we investigated the effect of cover plant diversity on OC contents of different soil aggregates, such as macro- (<2000–500 μm), meso- (<500–250 μm), and micro-aggregates (<250 μm). Our experiment included a total of 12 experimental treatments in triplicate; six different monoculture treatments such as chickling vetch (Vicia villosa), crimson clover (Trifolium incarnatum), hairy vetch (Vicia villosa), field peas (Pisum sativum), oilseed radish (Raphanus sativus), and mighty mustard (Brassica juncea), and their three- and six-species mixture treatments, including one unplanted control treatment. We performed this experiment usingdeep pots that contained soil collected from a corn-soybean rotation field. At vegetative maturity of cover plants (about 70 days), we took soil samples, and the soil aggregate-size classes were separated by the dry sieving. We hypothesized that cover crop type and diversity will improve OC contents of different soil aggregate-size classes. We found that cover plant species richness weakly positively increased OC contents of soil macro-aggregates (p = 0.056), whereas other aggregate-size classes did not respond to cover crop diversity gradient. Similarly, the OC contents of macroaggregates varied significantly (p = 0.013) under cover crop treatments, though neither monoculture nor mixture treatments showed significantly higher OC contents than the control treatment in this short-term experiment. Interestingly, the inclusion of hairy vetch and oilseed radish increased and decreased the OC contents of macro- and micro-aggregates, respectively. Moreover, we found a positive correlation between shoot biomass and OC contents of macroaggregates. Overall, our results suggest that species-rich rather than -poor communities may improve OC contents of soil macroaggregates, which constitute a major portion of soil systems, and are also considered as important indicators of soil functions.

Cholera is an acute diarrhoeal disease caused by Vibrio cholerae. It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact V. cholerae, namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of V. cholerae, we long-read sequenced 273 V. cholerae genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major V. cholerae lineages were identified: three known lineages, BD-1, BD-2a and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, at which point it had replaced BD-2 as the most common lineage in Bangladesh. We show that, in 2018, BD-1 was already predominant in the five northern regions, including Dhaka, consistent with an origin from northern India. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, yet persisted throughout the sampling period. Genes previously associated with antibiotic resistance in V. cholerae isolated from Bangladesh in the prior decade were entirely absent from all lineages in 2018–2019, suggesting shifting costs and benefits of encoding these genes. Our results highlight the diverse nature of the V. cholerae pangenome and geographic structure within a single outbreak season. This diversity provides the raw material for adaptation to antibiotics, phages and other selective pressures.

Rhizosphere soil ecosystems are represented by the diversity of different soil aggregate-size classes, such as large macroaggregates, small macroaggregates, mesoaggregates, and microaggregates. Though these aggregate-size classes represent distinct biological, chemical, and physical properties, little is known about their dynamics and relationships with belowground and aboveground plant traits. In this study, we examined the relationships of various soil aggregate-size classes and their organic carbon contents with many aboveground and belowground soybean plant traits. Our study revealed several novel and interesting relationships between soil structural properties and plant traits. Notably, small macroaggregates represented a major portion of the rhizosphere soil ecosystem of soybean plants while organic carbon contents decreased with decreasing size of soil aggregates. Only microaggregates showed a significant relationship with root architectural traits, such as length and surface area. Among all soil aggregate size classes, the abundance of small macroaggregates and the organic carbon contents of microaggregates were better correlated with plant traits. In general, organic carbon contents of different soil aggregate-size classes showed positive correlations with leaf trichome density (defense traits) and major macronutrients, such as root P, K, and S contents; while there were mostly negative correlations with some micronutrient (Ca, Mn, Zn, Cu, B, and Mg) contents of roots and shoots. However, the abundance of small macroaggregates mostly positively correlated with the mineral contents of plant roots and shoots. Collectively, the positive and negative correlations of organic carbon contents of different soil aggregate-size classes with trichomes (defense) and physiological traits (micro-mineral contents) suggest their significance in plant nutrition and defense. Though our results suggest the relationships of soil aggregate properties with aboveground and belowground traits, further research is needed to discern the role of soil structural traits in mediating plant growth, development, defense, and physiology.