Microbial genetic resources in food security to face COVID-19 pandemic

<p>COVID-19 has had an impact on the regional and worldwide agricultural value chain, jeopardizing food security. It is time to reassess the approach of the agri-food sector and to consider that the food supply and plant health, as agrosystemic services, must depend on strategies with a low impact on productive and environmental assets. One strategy is the use and optimization of microbial genetic resources (MGR) related to agroecosystems as a source of balance, functionality, productivity, inhibition of the impact of pests and pathogens, and contribution to the profitability of agri-food activity. It is necessary to strengthen and develop regional agricultural systems that are dynamic, that mitigate damages to the environment and produce nutritional and nutraceutical foods that ensure human health. Agricultural sciences are undergoing changes in scientific paradigms that will benefit the agri-food sector if we are able to learn from the impacts of an extensive technological agriculture. Approaching agriculture from an agro-systemic point of view in which the crop-community is the functional biological unit of study and to preserve the MGR diversity are the greatest challenges to create sustainable and resilient strategies and technologies that contribute towards human health and help prevent risks during health crises such as the ongoing COVID-19 pandemic.</p>

The Summing Up: The Astonishing Successes of the LMB and the Dawn of a New Structural Biological Era

The contrast between the related pre-World War II attitudes to scientific research and those of the current era are described and how this affects modern research. There follows a summary of the numerous major achievements in advanced research conducted at the Laboratory of Molecular Biology (LMB) from its existence as a biological unit at the Cavendish Laboratory from 1957 onwards. The impressive commercial successes of the LMB, made possible by recent changes in the policy of the Medical Research Council, are also outlined. The second half of the chapter describes the arrival, importance, and immense potential of electron cryo-microscopy (which is described in a non-technical manner) in structural molecular biology, with examples drawn from the study of neurodegenerative diseases and other areas of biology.

Assessing effects of genetic, environmental, and biotic gradients in species distribution modelling

To develop more reliable marine species distribution models (SDMs), we examine how genetic, climatic, and biotic interaction gradients give rise to prediction error in marine SDM. Genetic lineages with distinct ecological requirements spanning genetic gradients have yet to be treated separately in marine SDM, which are often constrained to modeling the potential distribution of one biological unit (e.g. lineage or species) at a time. By comparing SDM performance for the whole species or where observation and predictions were partitioned among geographically discontinuous genetic lineages, we first identified the appropriate biological unit for modeling sea scallop. Prediction errors, in particular contiguous omissions at the northern range margins were effectively halved in genetic lineage SDM (Total error=15%) verses whole species SDM. Remaining SDM prediction error was strongly associated with: i) Sharp climatic gradients (abrupt and persistent spatial shifts in limiting temperatures) found within continental shelf breaks and bottom channels. ii) A biotic gradient in the predation of sea scallop juveniles by the sand star within the Hudson Shelf USA. Our findings highlight how the accuracy of marine SDM is dependent on capturing the appropriate biological unit for modeling (e.g. lineages rather than species) and adequately resolving limiting abiotic and biotic interaction gradients.

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.

Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat

ABSTRACTIn the first longitudinal study of bat microbiomes, we find that unlike the pattern described in humans and other mammals, the prominent dynamics in Egyptian fruit bats’ fur microbiomes are those of change over time at the level of the colony as a whole. Thus, on average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats’ ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats’ fur, but differs from the more individualized pattern found in the bats’ gut microbiome.

Plasmids, Viruses, And Other Circular Elements In Rat Gut

Circular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 small, novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level.

Microbiotal-Host Interactions and Hypertension

Hypertension, or elevated blood pressure (BP), has been extensively researched over decades and clearly demonstrated to be caused due to a combination of host genetic and environmental factors. Although much research remains to be conducted to pin-point the precise genetic elements on the host genome that control BP, new lines of evidence are emerging to indicate that, besides the host genome, the genomes of all indigenous commensal micro-organisms, collectively referred to as the microbial metagenome or microbiome, are important, but largely understudied, determinants of BP. Unlike the rigid host genome, the microbiome or the “second genome” can be altered by diet or microbiotal transplantation in the host. This possibility is attractive from the perspective of exploiting the microbiotal composition for clinical management of inherited hypertension. Thus, focusing on the limited current literature supporting a role for the microbiome in BP regulation, this review highlights the need to further explore the role of the co-existence of host and the microbiota as an organized biological unit called the “holobiont” in the context of BP regulation.