Bacterial adhesion is the initial step in surface colonization and community formation. At the single-cell level, atomic force microscopy (AFM) techniques have enabled the quantification of adhesive forces between bacteria and substrata. However, conventional techniques depend on the irreversible immobilization of cells onto cantilevers, thus hampering throughput. Here, we developed a modular AFM method to reversibly immobilize functionalized beads as surface mimic and to probe adhesion of individual bacteria. We performed single-cell force spectroscopies with phylogenetically diverse leaf isolates of various size and morphology. Adhesion measurement of 28 bacterial strains revealed large differences in hydrophobic interactions of about three orders of magnitude. The highest adhesion forces of up to 50 nN were recorded for members of the Gammaproteobacteria. The hydrophobicity of the different isolates correlated positively with the retention of bacteria observed in planta and might provide a basis for successful leaf colonization and potentially disease outbreaks of pathogens.

Background

European forests are considered a crucial resource for supplying biomass to a growing bio-economy in Europe. This study aimed to assess the potential availability of forest biomass from European forests and its spatial distribution. We tried to answer the questions (i) how is the potential forest biomass availability spatially distributed across Europe and (ii) where are hotspots of potential forest biomass availability located?

Methods

The spatial distribution of woody biomass potentials was assessed for 2020 for stemwood, residues (branches and harvest losses) and stumps for 39 European countries. Using the European Forest Information SCENario (EFISCEN) model and international forest statistics, we estimated the theoretical amount of biomass that could be available based on the current and future development of the forest age-structure, growing stock and increment and forest management regimes. We combined these estimates with a set of environmental (site productivity, soil and water protection and biodiversity protection) and technical (recovery rate, soil bearing capacity) constraints, which reduced the amount of woody biomass that could potentially be available. We mapped the potential biomass availability at the level of administrative units and at the 10 km × 10 km grid level to gain insight into the spatial distribution of the woody biomass potentials.

Results

According to our results, the total availability of forest biomass ranges between 357 and 551 Tg dry matter per year. The largest potential supply of woody biomass per unit of land can be found in northern Europe (southern Finland and Sweden, Estonia and Latvia), central Europe (Austria, Czech Republic, and southern Germany), Slovenia, southwest France and Portugal. However, large parts of these potentials are already used to produce materials and energy. The distribution of biomass potentials that are currently unused only partially coincides with regions that currently have high levels of wood production.

Conclusions

Our study shows how the forest biomass potentials are spatially distributed across the European continent, thereby providing insight into where policies could focus on an increase of the supply of woody biomass from forests. Future research on potential biomass availability from European forests should also consider to what extent forest owners would be willing to mobilise additional biomass from their forests and at what costs the estimated potentials could be mobilised.

Interferon regulatory factors (IRFs) are transcription factors of the interferon (IFN)-inducible signaling pathway essential for host immunity against antimicrobial infection by virus and bacteria. Interferon regulatory factor 3 (IRF3) regulates the expression of IFNs and IFN-stimulated genes by binding to the IFN stimulatory response element (ISRE). In this study, we analyze the thymus transcriptome of the mandarin fish Siniperca chuatsi and report the functional analysis of Irf3 from the thymus as an emerging model of antiviral approaches. The predicted S. chuatsi IRF3 (Sc-Irf3) protein has 465 amino acid residues and evolutionarily conserved domains and is clustered in the IRF3 subfamily on a phylogenetic tree. Sc-Irf3 upon transgenic expression was mainly found in the cytoplasm through Western blot analysis and microscopy, but it translocated to the nucleus after polyinosinic:polycytidylic acid (ploly I:C) treatment. Endogenous Sc-irf3 RNA expression was detected in all eight adult organs examined. Importantly, Sc-irf3 RNA expression was significantly upregulated by ploly(I:C) treatment in the adult organs. Concurrently, reporter assays revealed that Sc-Irf3 increased the transcriptional activity of the ifnβ promoter, a minimal ISRE-containing promoter, and ifn promoter of mandarin fish. Therefore, Sc-Irf3 plays a major role in the IFN immune defense system against virus infection.

The vast majority of bacteria, including human pathogens and microbiome species, lack genetic tools needed to systematically associate genes with phenotypes. This is the major impediment to understanding the fundamental contributions of genes and gene networks to bacterial physiology and human health. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a versatile method of blocking gene expression using a catalytically inactive Cas9 protein (dCas9) and programmable single guide RNAs, has emerged as a powerful genetic tool to dissect the functions of essential and non-essential genes in species ranging from bacteria to humans^1–6. However, the difficulty of establishing effective CRISPRi systems across bacteria is a major barrier to its widespread use to dissect bacterial gene function. Here, we establish ‘Mobile-CRISPRi’, a suite of CRISPRi systems that combines modularity, stable genomic integration and ease of transfer to diverse bacteria by conjugation. Focusing predominantly on human pathogens associated with antibiotic resistance, we demonstrate the efficacy of Mobile-CRISPRi in gammaproteobacteria and Bacillales Firmicutes at the individual gene scale, by examining drug–gene synergies, and at the library scale, by systematically phenotyping conditionally essential genes involved in amino acid biosynthesis. Mobile-CRISPRi enables genetic dissection of non-model bacteria, facilitating analyses of microbiome function, antibiotic resistances and sensitivities, and comprehensive screens for host–microorganism interactions.

Bryozoan records from the shores and upper shelf (≤50 m depth) of the remote Azores Archipelago (central North Atlantic) have been analyzed, along with unpublished data and data from recent surveys. A checklist of 67 shallow-water species is hereby compiled for the region, of which more than one third represent records from campaigns conducted during the last 20 years. A classification on the origin of the species indicates that the majority (62%) are cryptogenic while 27% (n = 18) are considered native. Given the natural limitations for genetic exchange between the archipelago’s bryozoan populations and those from neighboring shores, the taxa presently considered as cryptogenic may yield a considerable amount of endemic species after taxonomic revision. The remaining 11% are confirmed as non-indigenous species, highlighting the importance of human-mediated transport in considerably enhancing the diversity of bryozoans in remote oceanic archipelagos, which would otherwise be off-limits to their natural dispersal capacity. In view of the need to quantitatively evaluate the certainty of species-level identification when assembling such biodiversity inventories, we have developed a method to attribute a degree of certainty to species records. The application of this method to the current checklist highlights the importance of further studies to ascertain the identification of many species recorded for the Azores, and to be able to categorize them confidently as either native, cryptogenic or non-indigenous.

Mosses, the pioneer member among the terrestrial plants, acquired remarkable adaptive advantages for their habitat transition and thus enjoy a global distribution even under diverse ecological conditions. Lipids are assumed to play a significant role in the development of various adaptive strategies that favour evolution. The present paper is an attempt to understand the possible reorientation of fatty acid machinery by the cellular system of the mosses that can be relevant in view of their eco-geographical diversity and distribution. Six abundant mosses were collected from dry, low lands of Hungarian plain, and six representative species belonging to similar systematic positions were collected from high-altitude, humid places of Eastern Himalayan Biodiversity Hotspot depending on their availability for experimentation. Total lipids of the plant samples were extracted, and the fatty acid compositions were analysed using gas chromatography–mass spectrometry and gas chromatography–flame ionizing detector. Chemical analyses revealed a diverse array of saturated, monounsaturated, long-chain polyunsaturated fatty acids in Eastern Himalayan mosses but abundance of saturated fatty acids in Hungarian mosses. One-way analysis of variance and principal component analysis based on various parameters of total fatty acid fingerprints clearly distinguished these two groups of mosses. Thus, this investigation concluded that fatty acid dynamicity has a possible role for adaptation of mosses under different climatic conditions.

Context

Herbicide treatments in viticulture can generate highly contrasting mosaics of vegetated and bare vineyards, of which vegetated fields often provide better conditions for biodiversity. In southern Switzerland, where herbicides are applied at large scales, vegetated vineyards are limited in extent and isolated from one another, potentially limiting the distribution and dispersal ability of organisms.

Objectives

We tested the separate and interactive effects of habitat amount and fragmentation on invertebrate abundance using a multi-scale framework, along with additional environmental factors. We identified which variables at which scales were most important in predicting patterns of invertebrate abundance.

Methods

We used a factorial design to sample across a gradient of habitat amount (area of vegetated vineyards, measured as percentage of landscape PLAND) and fragmentation (number of vegetated patches, measured as patch density PD). Using 10 different spatial scales, we identified the factors and scales that most strongly predicted invertebrate abundance and tested potential interactions between habitat amount and fragmentation.

Results

Habitat amount (PLAND index) was most important in predicting invertebrate numbers at a field scale (50 m radius). In contrast, we found a negative effect of fragmentation (PD) at a broad scale of 450 m radius, but no interactive effect between the two.

Conclusions

The spatial scales at which habitat amount and fragmentation affect invertebrates differ, underpinning the importance of spatially explicit study designs in disentangling the effects between habitat amount and configuration. We showed that the amount of vegetated vineyards has more influence on invertebrate abundance, but that fragmentation also contributed substantially. This suggests that efforts for augmenting the area of vegetated vineyards is more beneficial for invertebrate numbers than attempts to connect them.

The development of osmoregulatory and gas exchange organs was studied in larval yellowfin tuna (Thunnus albacares) from 2 to 25 days post-hatching (2.9–24.5 mm standard length, SL). Cutaneous and branchial ionocytes were identified using Na⁺/K⁺-ATPase immunostaining and scanning electron microscopy. Cutaneous ionocyte abundance significantly increased with SL, but a reduction in ionocyte size and density resulted in a significant decrease in relative ionocyte area. Cutaneous ionocytes in preflexion larvae had a wide apical opening with extended microvilli; however, microvilli retracted into an apical pit from flexion onward. Lamellae in the gill and pseudobranch were first detected ~ 3.3 mm SL. Ionocytes were always present on the gill arch, first appeared in the filaments and lamellae of the pseudobranch at 3.4 mm SL, and later in gill filaments at 4.2 mm SL, but were never observed in the gill lamellae. Unlike the cutaneous ionocytes, gill and pseudobranch ionocytes had a wide apical opening with extended microvilli throughout larval development. The interlamellar fusion, a specialized gill structure binding the lamellae of ram-ventilating fish, began forming by ~ 24.5 mm SL and contained ionocytes, a localization never before reported. Ionocytes were retained on the lamellar fusions and also found on the filament fusions of larger sub-adult yellowfin tuna; however, sub-adult gill ionocytes had apical pits. These results indicate a shift in gas exchange and NaCl secretion from the skin to branchial organs around the flexion stage, and reveal novel aspects of ionocyte localization and morphology in ram-ventilating fishes.