New frontiers in agriculture productivity : optimised microbial inoculants and in situ microbiome engineering

Increasing agricultural productivity is critical to feed the ever-growing humanpopulation. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability

Plant microbiomes : do different preservation approaches and primer sets alter our capacity to assess microbial diversity and community composition?

The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes

Distinct microbiota dysbiosis in patients with non-erosive reflux disease and esophageal adenocarcinoma

Non-erosive reflux disease (NERD) and esophageal adenocarcinoma (EAC) are often regarded as bookends in the gastroesophageal reflux disease spectrum. However, there is limited clinical evidence to support this disease paradigm while the underlying mechanisms of disease progression remain unclear. In this study, we used 16S rRNA sequencing and mass-spectrometer-based proteomics to characterize the esophageal microbiota and host mucosa proteome, respectively. A total of 70 participants from four patient groups (NERD, reflux esophagitis, Barrett’s esophagus, and EAC) and a control group were analyzed. Our results showed a unique NERD microbiota composition, distinct to control and other groups. We speculate that an increase in sulfate-reducing Proteobacteria and Bacteroidetes along with hydrogen producer Dorea are associated with a mechanistic role in visceral hypersensitivity. We also observed a distinct EAC microbiota consisting of a high abundance of lactic acid-producing bacteria (Staphylococcus, Lactobacillus, Bifidobacterium, and Streptococcus), which may contribute towards carcinogenesis through dysregulated lactate metabolism. This study suggests the close relationship between esophageal mucosal microbiota and the appearance of pathologies of this organ

Efficiency of two fragments of VP28 against White Spot Syndrome Virus in Litopenaeus vannamei

White Spot Syndrome Virus (WSSV) is a major pathogen in shrimp culture, which is widespread in China, Southeast Asia and India continent, causing a catastrophic economical loss in shrimp aquaculture. In the present study, VP28 caused effective approaches in the systemic infection of WSSV in shrimp. To define the key regions of VP28 responsible for shrimp immune, N-terminal and C-terminal fragments of VP28 were constructed and expressed in Escherichia coli. The protective efficacy of injection and oral feeding of two fragments in Litopenaeus vannamei was investigated. Quantitative real-time PCR was used to determine the mRNA expression level of STAT, Dicer, Argonaute and Lysozyme in different tissues, and relevant enzyme activity was determined from the hemolymph after immunization. Vaccination experiments indicated that C-terminal VP28 shows significant effect against WSSV compared with that of N-terminal VP28. Dicer, STAT, Argonaute and Lysozyme in C-terminal VP28 treated groups have higher mRNA expression compared with that of N-terminal VP28 treated groups. Results suggested that C-terminal VP28 might play a crucial role in the pathway of viral attack

White spot syndrome virus VP12 interacts with adenine nucleotide translocase of Litopenaeus vannamei

White spot syndrome virus VP12 contains cell attachment motif RGD which is considered to be critical for host cell binding. Until now, the function of this protein remains undefined. In this study, we explored the interaction of VP12 with host cells. A new shrimp protein (adenine nucleotide translocase of Litopenaeus vannamei, LvANT) is selected by far-western overlay assay. Tissue distribution of adenine nucleotide translocase mRNA showed that it was commonly spread in all the tissues detected. Cellular localization of LvANT in shrimp hemocytes showed that it was primarily located in the cytoplasm of hemocytes and colocalized with mitochondria. ELISA and far-western blot assay confirmed that VP12 interacted with LvANT. In vivo neutralization assay showed that anti-LvANT antibody can significantly reduce the mortality of shrimp challenged by WSSV at 48 h post-treatment. Our results collectively showed that VP12 is involved in host cell binding via interaction with adenine nucleotide translocase

Microbiome-mediated stress resistance in plants

Plants are subjected to diverse biotic and abiotic stresses in life. These can induce changes in transcriptomics and metabolomics, resulting in changes to root and leaf exudates and, in turn, altering the plant-associated microbial community. Emerging evidence demonstrates that changes, especially the increased abundance of commensal microbes following stresses, can be beneficial for plant survival and act as a legacy, enhancing offspring fitness. However, outstanding questions remain regarding the microbial role in plant defense, many of which may now be answered utilizing a novel synthetic community approach. In this article, building on our current understanding on stress-induced changes in plant microbiomes, we propose a ‘DefenseBiome’ concept that informs the design and construction of beneficial microbial synthetic communities for improving fundamental understanding of plant–microbial interactions and the development of plant probiotics