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The management of plant diseases are dependent on a variety of factors. Two important variables are the soil quality and its bacterial/fungal community. However, the interaction of these factors is not well understood and remains problematic in producing healthy crops. Here, the effect of oak–bark compost, Bacillus subtilis subsp. subtilis, Trichoderma harzianum and two commercial products (FZB24 and FZB42) were investigated on tomato growth, production of metabolites and resistance under biotic stress condition (infection with Phytophthora infestans). Oak–bark compost, B. subtilis subsp. subtilis, and T. harzianum significantly enhanced plant growth and immunity when exposed to P. infestans. However, the commercial products were not as effective in promoting growth, with FZB42 having the weakest protection. Furthermore, elevated levels of anthocyanins did not correlate with enhanced plant resistance. Overall, the most effective and consistent plant protection was obtained when B. subtilis subsp. subtilis was combined with oak–bark compost. In contrast, the combination of T. harzianum and oak–bark compost resulted in increased disease severity. The use of compost in combination with bio-agents should, therefore, be evaluated carefully for a reliable and consistent tomato protection.

Access to greater genomic resolution through new sequencing technologies is transforming the field of plant pathology. As scientists embrace these new methods, some overarching patterns and observations come into focus. Evolutionary genomic studies are used to determine not only the origins of pathogen lineages and geographic patterns of genetic diversity, but also to discern how natural selection structures genetic variation across the genome. With greater and greater resolution, we can now pinpoint the targets of selection on a large scale. At multiple levels, crypsis and convergent evolution are evident. Host jumps and shifts may be more pervasive than once believed, and hybridization and horizontal gene transfer (HGT) likely play important roles in the emergence of genetic novelty.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into the current coronavirus disease pandemic. SARS-CoV-2 is a respiratory virus that causes symptoms similar to those caused by influenza A and B viruses. On July 2, 2020, the US Food and Drug Administration granted emergency use authorization for in vitro diagnostic use of the Influenza SARS-CoV-2 Multiplex Assay. This assay detects influenza A virus at 102.0, influenza B virus at 102.2, and SARS-CoV-2 at 100.3 50% tissue culture or egg infectious dose, or as few as 5 RNA copies/reaction. The simultaneous detection and differentiation of these 3 major pathogens increases overall testing capacity, conserves resources, identifies co-infections, and enables efficient surveillance of influenza viruses and SARS-CoV-2.

Background The LysM receptor-like kinases (LysM-RLKs) are important to both plant defense and symbiosis. Previous studies described three clades of LysM-RLKs: LysM-I/LYKs (10+ exons per gene and containing conserved kinase residues), LysM-II/LYRs (1–5 exons per gene, lacking conserved kinase residues), and LysM-III (two exons per gene, with a kinase unlike other LysM-RLK kinases and restricted to legumes). LysM-II gene products are presumably not functional as conventional receptor kinases, but several are known to operate in complexes with other LysM-RLKs. One aim of our study was to take advantage of recently mapped wild tomato transcriptomes to evaluate the evolutionary history of LysM-RLKs within and between species. The second aim was to place these results into a broader phylogenetic context by integrating them into a sequence analysis of LysM-RLKs from other functionally well-characterized model plant species. Furthermore, we sought to assess whether the Group III LysM-RLKs were restricted to the legumes or found more broadly across Angiosperms. Results Purifying selection was found to be the prevailing form of natural selection within species at LysM-RLKs. No signatures of balancing selection were found in species-wide samples of two wild tomato species. Most genes showed a greater extent of purifying selection in their intracellular domains, with the exception of Sl LYK3 which showed strong purifying selection in both the extracellular and intracellular domains in wild tomato species. The phylogenetic analysis did not reveal a clustering of microbe/functional specificity to groups of closely related proteins. We also discovered new putative LysM-III genes in a range of Rosid species, including Eucalyptus grandis . Conclusions The LysM-III genes likely originated before the divergence of E. grandis from other Rosids via a fusion of a Group II LysM triplet and a kinase from another RLK family. Sl LYK3 emerges as an especially interesting candidate for further study due to the high protein sequence conservation within species, its position in a clade of LysM-RLKs with distinct LysM domains, and its close evolutionary relationship with LYK3 from Arabidopsis thaliana .

As key-players of plant immunity, the proteins encoded by resistance genes ( -genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some -genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by -genes is triggered by pathogen infection is currently an open question. In this study we analyzed the expression of 940 -genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence -gene expression in plants. We found that most -genes are expressed at a low level. A small subset of -genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These -genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all -genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in -gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes. These results call into question the widespread view that -gene expression is induced upon pathogen attack. Instead, a small core set of -genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.

A SARS-CoV-2 outbreak at a meat processing plant (MPP) in the German district of Gütersloh accounted for 18% of Germany’s SARS-CoV-2 cases in June 2020 and was subject of intense public interest, including the speculation that the outbreak strain may have been imported by foreign MPP workers. We sequenced the SARS-CoV-2 genomes of 1,438 SARS-CoV-2 samples collected from Gütersloh MPP workers for serial diagnostic testing and screening purposes (“outbreak samples”; approximate case coverage 68%) and of 157 samples collected from Gütersloh-area cases for routine diagnostic purposes (“community samples”). Greater than 98% of outbreak samples carried the outbreak-associated strain, defined by eight mutations and lineage B.1.329, confirming the overall clonality of the outbreak and showing that potential secondary introductions of other viral lineages had an at most limited role. Of fifteen viral sub-lineages detected in early outbreak-associated samples sequenced by another study, only one showed substantial persistence into the peak outbreak period, suggesting that transmission dynamics within the MPP were influenced by bottlenecks and superspreading-like patterns. While the detection of B.1.329 in community samples peaked during the outbreak, it was found to be present in community samples between March and September 2020, with the first exact matches to the outbreak strain appearing in April 2020. We found no epidemiological connections between early B.1.329-carrying community cases and the MPP, and a GISAID search for B.1.329 did not identify any samples collected outside of Germany. The outbreak strain was therefore likely circulating within the community before the outbreak and there was no indication of importation by MPP workers. Our study demonstrates how large-scale viral genome sequencing can contribute to the investigation of outbreaks and inform public discourse.

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant-pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the \"Guard-Hypothesis,\" R proteins (the \"guards\") can sense modification of target molecules in the host (the \"guardees\") by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the \"guardee-effector\" interface for pathogen recognition, natural selection acts on the \"guard-guardee\" interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen.

The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and Phytophthora cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys, and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud‐F (Mycologia, 2000) and a reverse primer found using DegePrime (Applied and Environmental Microbiology, 2014). Factors reflecting topo‐edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and P. cinnamomi, both displaying strong site‐specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlight the importance to study oomycete communities in relation to such ecological patterns. The phylum Oomycota comprises important tree pathogens, but knowledge on environmental factors that could explain their community patterns is scarce. To advance our understanding, oomycetes in the oak rhizosphere were studied using metabarcoding of the taxonomic marker cytochrome c oxidase subunit II and linked to biotic and abiotic variables. Oomycete communities were strongly correlated with the environmental factors altitude, crown foliation, slope and soil skeleton and soil nitrogen.

The perception of downy mildew avirulence (Arabidopsis thaliana Recognized [ATR]) gene products by matching Arabidopsis thaliana resistance (Recognition of Peronospora parasitica [RPP]) gene products triggers localized cell death (a hypersensitive response) in the host plant, and this inhibits pathogen development. The oomycete pathogen, therefore, is under selection pressure to alter the form of these gene products to prevent detection. That the pathogen maintains these genes indicates that they play a positive role in pathogen survival. Despite significant progress in cloning plant RPP genes and characterizing essential plant components of resistance signaling pathways, little progress has been made in identifying the oomycete molecules that trigger them. Concluding a map-based cloning effort, we have identified an avirulence gene, ATR1[superscript NdWsB], that is detected by RPP1 from the Arabidopsis accession Niederzenz in the cytoplasm of host plant cells. We report the cloning of six highly divergent alleles of ATR1[superscript NdWsB] from eight downy mildew isolates and demonstrate that the ATR1[superscript NdWsB] alleles are differentially recognized by RPP1 genes from two Arabidopsis accessions (Niederzenz and Wassilewskija). RPP1-Nd recognizes a single allele of ATR1[superscript NdWsB]; RPP1-WsB also detects this allele plus three additional alleles with divergent sequences. The Emco5 isolate expresses an allele of ATR1[superscript NdWsB] that is recognized by RPP1-WsB, but the isolate evades detection in planta. Although the Cala2 isolate is recognized by RPP1-WsA, the ATR1[superscript NdWsB] allele from Cala2 is not, demonstrating that RPP1-WsA detects a novel ATR gene product. Cloning of ATR1[superscript NdWsB] has highlighted the presence of a highly conserved novel amino acid motif in avirulence proteins from three different oomycetes. The presence of the motif in additional secreted proteins from plant pathogenic oomycetes and its similarity to a host-targeting signal from malaria parasites suggest a conserved role in pathogenicity.