Bacterial chitin degradation-mechanisms and ecophysiological strategies

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

Eco-friendly and safe alternatives for the valorization of shrimp farming waste

The seafood industry generates waste, including shells, bones, intestines, and wastewater. The discards are nutrient-rich, containing varying concentrations of carotenoids, proteins, chitin, and other minerals. Thus, it is imperative to subject seafood waste, including shrimp waste (SW), to secondary processing and valorization for demineralization and deproteination to retrieve industrially essential compounds. Although several chemical processes are available for SW processing, most of them are inherently ecotoxic. Bioconversion of SW is cost-effective, ecofriendly, and safe. Microbial fermentation and the action of exogenous enzymes are among the significant SW bioconversion processes that transform seafood waste into valuable products. SW is a potential raw material for agrochemicals, microbial culture media, adsorbents, therapeutics, nutraceuticals, and bio-nanomaterials. This review comprehensively elucidates the valorization approaches of SW, addressing the drawbacks of chemically mediated methods for SW treatments. It is a broad overview of the applications associated with nutrient-rich SW, besides highlighting the role of major shrimp-producing countries in exploring SW to achieve safe, ecofriendly, and efficient bio-products.

Chitinases: expanding the boundaries of knowledge beyond routinized chitin degradation

Chitinases, enzymes that degrade chitin, have long been studied for their role in various biological processes. They play crucial roles in the moulting process of invertebrates, the digestion of chitinous food, and defense against chitin-bearing pathogens. Additionally, chitinases are involved in physiological functions in crustaceans, such as chitinous food digestion, moulting, and stress response. Moreover, chitinases are universally distributed in organisms from viruses to mammals and have diverse functions including tissue degradation and remodeling, nutrition uptake, pathogen invasion, and immune response regulation. The discovery of these diverse functions expands our understanding of the biological significance and potential applications of chitinases. However, recent research has shown that chitinases possess several other functions beyond just chitin degradation. Their potential as biopesticides, therapeutic agents, and tools for bioremediation underscores their significance in addressing global challenges. More importantly, we noted that they may be applied as bioweapons if ethical regulations regarding production, engineering and application are overlooked.

Natural colorant incorporated biopolymers-based pH-sensing films for indicating the food product quality and safety

The current synthetic plastic-based packaging creates environmental hazards that impact climate change. Hence, the topic of the current research in food packaging is biodegradable packaging and its development. In addition, new smart packaging solutions are being developed to monitor the quality of packaged foods, with dual functions as food preservation and quality indicators. In the creation of intelligent and active food packaging, many natural colorants have been employed effectively as pH indicators and active substances, respectively. This review provides an overview of biodegradable polymers and natural colorants that are being extensively studied for pH-indicating packaging. A comprehensive discussion has been provided on the current status of the development of intelligent packaging systems for food, different incorporation techniques, and technical challenges in the development of such green packaging. Finally, the food industry and environmental protection might be revolutionized by pH-sensing biodegradable packaging enabling real-time detection of food product quality and safety.

Diversity and functional characteristics of culturable bacterial endosymbionts from cassava whitefly biotype Asia II-5, Bemisia tabaci

Whitefly Bemisia tabaci, a carrier of cassava mosaic disease (CMD), poses a significant threat to cassava crops. Investigating culturable bacteria and their impact on whiteflies is crucial due to their vital role in whitefly fitness and survival. The whitefly biotype associated with cassava and transmitting CMD in India has been identified as Asia II 5 through partial mitochondrial cytochrome oxidase I gene sequencing. In this study, bacteria associated with adult B. tabaci feeding on cassava were extracted using seven different media. Nutrient Agar (NA), Soyabean Casein Digest Medium (SCDM), Luria Bertani agar (LBA), and Reasoner's 2A agar (R2A) media resulted in 19, 6, 4, and 4 isolates, respectively, producing a total of 33 distinct bacterial isolates. Species identification through 16SrRNA gene sequencing revealed that all isolates belonged to the Bacillota and Pseudomonadota phyla, encompassing 11 genera: Bacillus, Cytobacillus, Exiguobacterium, Terribacillus, Brevibacillus, Enterococcus, Staphylococcus, Brucella, Novosphingobium, Lysobacter, and Pseudomonas. All bacterial isolates were tested for chitinase, protease, siderophore activity, and antibiotic sensitivity. Nine isolates exhibited chitinase activity, 28 showed protease activity, and 23 displayed siderophore activity. Most isolates were sensitive to antibiotics such as Vancomycin, Streptomycin, Erythromycin, Kanamycin, Doxycycline, Tetracycline, and Ciprofloxacin, while they demonstrated resistance to Bacitracin and Colistin. Understanding the culturable bacteria associated with cassava whitefly and their functional significance could contribute to developing effective cassava whitefly and CMD control in agriculture.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03949-0.

Exploring the potential of jujube seed powder in polysaccharide based functional film: Characterization, properties and application in fruit preservation

In this study, we fabricated a novel biodegradable functional film using natural polysaccharides by adding jujube seed powder as an active ingredient. Scanning electron microscopy analysis showed agglomerate formation in the film with increasing concentration of seed powder. Fourier transform-infrared spectroscopy study demonstrated an electrostatic interaction between pectin and chitosan. The water solubility and swelling degree significantly decreased from 55.5 to 47.7 % and 66.0 to 41.9 %, respectively, depicting the film's water resistance properties. Higher opacity and lower transmittance value of the film indicated its protective effect towards light-induced oxidation of food. It was observed that the fabricated active film biodegraded to 82.33 % in 6 days. The DPPH radical scavenging activity of 98.02 % was observed for the functional film. The film showed antifungal activity against B. cinerea and P. chrysogenum. The highest zone of inhibition was obtained against food spoiling bacteria B. subtilis followed by S. aureus, P. aeruginosa and E. coli. Genotoxicity studies with the fabricated film showed a mitotic index of 8 % compared to 3 % in the control film. We used the fabricated film to preserve grapefruits, and the result showed that it could preserve grapes for ten days with an increase in antioxidant activity and polyphenolic content.

Biodegradable bio-film based on Cordyceps militaris and metal-organic frameworks for fruit preservation

In this study, Cordyceps militaris matrix was employed for the first time to fabricate a biodegradable food packaging. Carmine and Ag@CuBTC were introduced to cross-link with mycelium and were uniformly dispersed within the matrix to enhance the water resistance, antimicrobial, and antioxidant properties of the bio-films. The bio-film displayed high biodegradability, with nearly 100 % degradation achieved after three weeks. The bio-film exhibited exceptional resistance to oxidation (49.30 % DPPH and 93.94 % ABTS•+), as well as effective inhibitory capabilities against E. coli and S. aureus, respectively. The composite film maintained a high CO2/O2 selective permeability, which was advantageous for mitigating fruit metabolism and extending shelf life. Simultaneously, food preservation experiments confirmed that these bio-films can decelerate the spoilage of fruits and effectively prolong the shelf-life of food. The experimental findings indicated that the prepared Bio-R-Ag@Cu film held promise as an environmentally friendly biodegradable material for food packaging.

Soil and seed both influence bacterial diversity in the microbiome of the Cannabis sativa seedling endosphere

Introduction

Phytobiomes have a significant impact on plant health. The microbiome of Cannabis sativa is particularly interesting both because of renewed interest in this crop and because it is commercially propagated in two different ways (i.e. clonally and by seed). Angiosperms obtain a founding population of seed-borne endophytes from their seed-bearing parent. This study examines the influence of both seed and soil-derived bacteria on the endospheres of cannabis seedlings of both hemp- and drug-types.

Methods

A multi-factorial metagenomic study was conducted with three cannabis genotypes and two soil sources, which were tested both before and after autoclave sterilization. Seedlings were grown on soil, then rinsed and surface-sterilized, and 16S rDNA amplicons from seedling endophytes were sequenced, taxonomically classified, and used to estimate alpha- and beta-diversity in Qiime2. The statistical significance of differences in seedling microbiomes across treatments was tested, and PiCRUST2 was used to infer the functional relevance of these differences.

Results

Soil was found to have a profound effect on the alpha-diversity, beta-diversity, relative abundance, and functional genes of endophytic bacteria in germinating cannabis seedlings. Additionally, there was a significant effect of cannabis genotype on beta diversity, especially when genotypes were grown in sterilized soil. Gammaproteobacteria and Bacilli were the two most abundant taxa and were found in all genotypes and soil types, including sterilized soil.

Discussion

The results indicated that a component of cannabis seedling endosphere microbiomes is seed-derived and conserved across the environments tested. Functional prediction of seedling endophytes using piCRUST suggested a number of important functions of seed-borne endophytes in cannabis including nutrient and amino acid cycling, hormone regulation, and as precursors to antibiotics. This study suggested both seed and soil play a critical role in shaping the microbiome of germinating cannabis seedlings.

Polysaccharide degradation in Cellvibrionaceae: Genomic insights of the novel chitin-degrading marine bacterium, strain KSP-S5-2, and its chitinolytic activity

In this study, we present the genome characterization of a novel chitin-degrading strain, KSP-S5-2, and comparative genomics of 33 strains of Cellvibrionaceae. Strain KSP-S5-2 was isolated from mangrove sediment collected in Balik Pulau, Penang, Malaysia, and its 16S rRNA gene sequence showed the highest similarity (95.09%) to Teredinibacter franksiae. Genome-wide analyses including 16S rRNA gene sequence similarity, average nucleotide identity, digital DNA-DNA hybridization, and phylogenomics, suggested that KSP-S5-2 represents a novel species in the family Cellvibrionaceae. The Cellvibrionaceae pan-genome exhibited high genomic variability, with only 1.7% representing the core genome, while the flexible genome showed a notable enrichment of genes related to carbohydrate metabolism and transport pathway. This observation sheds light on the genetic plasticity of the Cellvibrionaceae family and the gene pools that form the basis for the evolution of polysaccharide-degrading capabilities. Comparative analysis of the carbohydrate-active enzymes across Cellvibrionaceae strains revealed that the chitinolytic system is not universally present within the family, as only 18 of the 33 genomes encoded chitinases. Strain KSP-S5-2 displayed an expanded repertoire of chitinolytic enzymes (25 GH18, two GH19 chitinases, and five GH20 β-N-acetylhexosaminidases) but lacked genes for agar, xylan, and pectin degradation, indicating specialized enzymatic machinery focused primarily on chitin degradation. Further, the strain degraded 90% of chitin after 10 days of incubation. In summary, our findings provided insights into strain KSP-S5-2's genomic potential, the genetics of its chitinolytic system, genomic diversity within the Cellvibrionaceae family in terms of polysaccharide degradation, and its application for chitin degradation.

Activity of a Recombinant Chitinase of the Atta sexdens Ant on Different Forms of Chitin and Its Fungicidal Effect against Lasiodiplodia theobromae

This study evaluates the activity of a recombinant chitinase from the leaf-cutting ant Atta sexdens (AsChtII-C4B1) against colloidal and solid α- and β-chitin substrates. 1H NMR analyses of the reaction media showed the formation of N-acetylglucosamine (GlcNAc) as the hydrolysis product. Viscometry analyses revealed a reduction in the viscosity of chitin solutions, indicating that the enzyme decreases their molecular masses. Both solid state 13C NMR and XRD analyses showed minor differences in chitin crystallinity pre- and post-reaction, indicative of partial hydrolysis under the studied conditions, resulting in the formation of GlcNAc and a reduction in molecular mass. However, the enzyme was unable to completely degrade the chitin samples, as they retained most of their solid-state structure. It was also observed that the enzyme acts progressively and with a greater activity on α-chitin than on β-chitin. AsChtII-C4B1 significantly changed the hyphae of the phytopathogenic fungus Lasiodiplodia theobromae, hindering its growth in both solid and liquid media and reducing its dry biomass by approximately 61%. The results demonstrate that AsChtII-C4B1 could be applied as an agent for the bioproduction of chitin derivatives and as a potential antifungal agent.

Unveiling the Occurrence and Non-Negligible Role of Amino Sugars in Waste Activated Sludge Fermentation by an Enriched Chitin-Degradation Consortium

Polysaccharides in extracellular polymeric substances (EPS) can form a hybrid matrix network with proteins, impeding waste-activated sludge (WAS) fermentation. Amino sugars, such as N-acetyl-d-glucosamine (GlcNAc) polymers and sialic acid, are the non-negligible components in the EPS of aerobic granules or biofilm. However, the occurrence of amino sugars in WAS and their degradation remains unclear. Thus, amino sugars (∼6.0%) in WAS were revealed, and the genera of Lactococcus and Zoogloea were identified for the first time. Chitin was used as the substrate to enrich a chitin-degrading consortium (CDC). The COD balances for methane production ranged from 83.3 and 95.1%. Chitin was gradually converted to oligosaccharides and GlcNAc after dosing with the extracellular enzyme. After doing enriched CDC in WAS, the final methane production markedly increased to 60.4 ± 0.6 mL, reflecting an increase of ∼62%. Four model substrates of amino sugars (GlcNAc and sialic acid) and polysaccharides (cellulose and dextran) could be used by CDC. Treponema (34.3%) was identified as the core bacterium via excreting chitinases (EC 3.2.1.14) and N-acetyl-glucosaminidases (EC 3.2.1.52), especially the genetic abundance of chitinases in CDC was 2.5 times higher than that of WAS. Thus, this study provides an elegant method for the utilization of amino sugar-enriched organics.

Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil

Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92-47.9%), Proteobacteria (20.50-28.30%), and Chloroflexi (13.88-15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations.

Functional Comparison of Three Chitinases from Symbiotic Bacteria of Entomopathogenic Nematodes

Xenorhabdus and Photorhabdus, bacterial symbionts of entomopathogenic nematodes Steinernema and Heterorhabditis, respectively, have several biological activities including insecticidal and antimicrobial activities. Thus, XnChi, XhChi, and PtChi, chitinases of X. nematophila, X. hominickii, and P. temperata isolated from Korean indigenous EPNs S. carpocapsae GJ1-2, S. monticolum GJ11-1, and H. megidis GJ1-2 were cloned and expressed in Escherichia coli BL21 to compare their biological activities. Chitinase proteins of these bacterial symbionts purified using the Ni-NTA system showed different chitobiosidase and endochitinase activities, but N-acetylglucosamidinase activities were not shown in the measuring of chitinolytic activity through N-acetyl-D-glucosarmine oligomers. In addition, the proteins showed different insecticidal and antifungal activities. XnChi showed the highest insecticidal activity against Galleria mellonella, followed by PtChi and XhChi. In antifungal activity, XhChi showed the highest half-maximal inhibitory concentration (IC50) against Fusarium oxysporum with 0.031 mg/mL, followed by PtChi with 0.046 mg/mL, and XnChi with 0.072 mg/mL. XhChi also showed the highest IC50 against F. graminearum with 0.040 mg/mL, but XnChi was more toxic than PtChi with 0.055 mg/mL and 0.133 mg/mL, respectively. This study provides an innovative approach to the biological control of insect pests and fungal diseases of plants with the biological activity of symbiotic bacterial chitinases of entomopathogenic nematodes.

N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei

Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.

Identification and evaluation of CAZyme genes, along with functional characterization of a new GH46 chitosanase from Streptomyces sp. KCCM12257

The genomic analysis of Streptomyces sp. KCCM12257 presented 233 CAZyme genes with a predominant glycosyl hydrolase family. This contributes degradation of various polysaccharides including chitin and chitosan, and other promising candidates for the production of different oligosaccharides. We screened the strain providing different polysaccharides as a sole source of carbon and strain KCCM12257, showed higher activity towards colloidal chitosan. Further, we identified and characterized a new chitosanase (MDI5907146) of GH46 family. There was no activity towards chitin, carboxymethylcellulose, or even with chitosan powder. This enzyme acts on colloidal chitosan and hydrolyzes it down into monoacetyl chitobiose, which consists of two glucosamine units with an acetyl group attached to them. The maximum enzyme activity was observed at pH 6.5 and 40 °C using colloidal chitosan as a substrate. The Co2+ metal ions almost double the reaction as compared to other metal ions. The dissociation constant (Km) and of colloidal chitosan (≥90 % and ≥75%DD) were 3.03 mg/ml and 5.01 mg/ml respectively, while maximum velocity (Vmax) values were found to be 36 mg/ml, and 30 μM/μg/min, respectively. Similarly, catalytic efficiency (Kcat/Km) of colloidal chitosan with ≥90 %DD was 1.9 fold higher than colloidal chitosan with ≥75%DD.

Biodegradation of polysaccharide-based biocomposites with acetylated cellulose nanocrystals, alginate and chitosan in aqueous environment

Biocomposite films from renewable sources are seen to be viable candidates as sustainable, zero-waste packaging materials. In this study, biocomposites films using chitosan and alginate as matrices, and pristine or acetylated cellulose nanocrystals (CNCs) as reinforcement agents, were fabricated, thoroughly characterized in terms of structure (with ATR-FTIR and XRD), morphology (SEM), thermal stability (TGA coupled with FTIR), water content and solubility and mechanical properties and subjected to controlled biological degradation in aqueous environment with added activated sludge. Biodegradation activity was followed through respirometry by measurement of change in partial O2 pressure using OxiTop® system. While the initial rate of biodegradation is higher in chitosan-based films with incorporated CNCs (both pristine and modified) compared to any other tested biocomposites, it was observed that chitosan-based films are not completely degradable in activated sludge medium, whereas alginate-based films reached complete biodegradation in 107 h to 112 h. Additional study of the aqueous medium with in situ FTIR during biodegradation offered an insight into biodegradation mechanisms. Use of advanced statistical methods indicated that selection of material (ALG vs CH) has the highest influence on biodegradability, followed by solubility of the material and its thermal stability.

Gut microbiota in the short-beaked echidna (Tachyglossus Aculeatus) shows stability across gestation

Indigenous gut microbial communities (microbiota) play critical roles in health and may be especially important for the mother and fetus during pregnancy. Monotremes, such as the short-beaked echidna, have evolved to lay and incubate an egg, which hatches in their pouch where the young feeds. Since both feces and eggs pass through the cloaca, the fecal microbiota of female echidnas provides an opportunity for vertical transmission of microbes to their offspring. Here, we characterize the gut/fecal microbiome of female short-beaked echidnas and gain a better understanding of the changes that may occur in their microbiome as they go through pregnancy. Fecal samples from four female and five male echidnas were obtained from the Currumbin Wildlife Sanctuary in Queensland and sequenced to evaluate bacterial community structure. We identified 25 core bacteria, most of which were present in male and female samples. Genera such as Fusobacterium, Bacteroides, Escherichia-Shigella, and Lactobacillus were consistently abundant, regardless of sex or gestation stage, accounting for 58.00% and 56.14% of reads in male and female samples, respectively. The echidna microbiome remained stable across the different gestation stages, though there was a significant difference in microbiota composition between male and female echidnas. This study is the first to describe the microbiome composition of short-beaked echidnas across reproductive phases and allows the opportunity for this novel information to be used as a metric of health to aid in the detection of diseases triggered by microbiota dysbiosis.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis

BACKGROUND

The microbiota of multicellular organisms undergoes considerable changes during host ontogeny but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacterial recolonization experiments in Nematostella vectensis as a model to understand general mechanisms determining bacterial establishment and succession. We compared the dynamic establishment of the microbiome on the germfree host and on inert silicone tubes.

RESULTS

Following the dynamic reconstruction of microbial communities on both substrates, we show that the initial colonization events are strongly influenced by the host but not by the silicone tube, while the subsequent bacteria-bacteria interactions are the main driver of bacterial succession. Interestingly, the recolonization pattern on adult hosts resembles the ontogenetic colonization succession. This process occurs independently of the bacterial composition of the inoculum and can be followed at the level of individual bacteria. To identify potential metabolic traits associated with initial colonization success and potential metabolic interactions among bacteria associated with bacterial succession, we reconstructed the metabolic networks of bacterial colonizers based on their genomes. These analyses revealed that bacterial metabolic capabilities reflect the recolonization pattern, and the degradation of chitin might be a selection factor during early recolonization of the animal. Concurrently, transcriptomic analyses revealed that Nematostella possesses two chitin synthase genes, one of which is upregulated during early recolonization.

CONCLUSIONS

Our results show that early recolonization events are strongly controlled by the host while subsequent colonization depends on metabolic bacteria-bacteria interactions largely independent of host ontogeny. Video Abstract.

Chitin degradation by Synechococcus WH7803

Chitin is an abundant, carbon-rich polymer in the marine environment. Chitinase activity has been detected in spent media of Synechococcus WH7803 cultures-yet it was unclear which specific enzymes were involved. Here we delivered a CRISPR tool into the cells via electroporation to generate loss-of-function mutants of putative candidates and identified ChiA as the enzyme required for the activity detected in the wild type.

Tidal dynamics regulates potential coupling of carbon‑nitrogen‑sulfur cycling microbes in intertidal flats

Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.

Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data

Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.

Vibrio cyclitrophicus population-specific biofilm formation and epibiotic growth on marine copepods

Vibrio spp. form a part of the microbiome of copepods-an abundant component of marine mesozooplankton. The biological mechanisms of the Vibrio-copepod association are largely unknown. In this study we compared biofilm formation of V. cyclitrophicus isolated from copepods (L-strains related to other particle-associated strains) and closely related strains originating from seawater (S-strains), and visualized and quantified their attachment and growth on copepods. The S- and L-strains formed similar biofilms in the presence of complete sea salts, suggesting previously unknown biofilm mechanisms in the S-strains. No biofilms formed if sodium chloride was present as the only salt but added calcium significantly enhanced biofilms in the L-strains. GFP-L-strain cells attached to live copepods at higher numbers than the S-strains, suggesting distinct mechanisms, potentially including calcium, support their colonization of copepods. The cells grew on live copepods after attachment, demonstrating that copepods sustain epibiotic V. cyclitrophicus growth in situ. The results demonstrate that in spite of their 99.1% average nucleotide identity, these V. cyclitrophicus strains have a differential capacity to colonize marine copepods. The introduced V. cyclitrophicus-A. tonsa model could be informative in future studies on Vibrio-copepod association.

Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals

IMPORTANCE

Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.

Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos

Chitin is the most abundant natural polymer in the oceans, where it is primarily recycled by chitin-degrading microorganisms. Endozoicomonadaceae (Oceanospirillales) bacteria are prominent symbionts of sessile marine animals, particularly corals, and presumably contribute to nutrient cycling in their hosts. To reveal the chitinolytic potential of this iconic, animal-dwelling bacterial family, we examined 42 publicly available genomes of cultured and uncultured Endozoicomonadaceae strains for the presence of chitinase-encoding genes. Thirty-two of 42 Endozoicomonadaceae genomes harbored endo-chitinase- (EC 3.2.1.14), 25 had exo-chitinase- (EC 3.2.1.52) and 23 polysaccharide deacetylase-encoding genes. Chitinases were present in cultured and uncultured Endozoicomonadaceae lineages associated with diverse marine animals, including the three formally described genera Endozoicomonas, Paraendozoicomonas and Kistimonas, the new genus Candidatus Gorgonimonas, and other, yet unclassified, groups of the family. Most endo-chitinases belonged to the glycoside hydrolase family GH18 but five GH19 endo-chitinases were also present. Many endo-chitinases harbored an active site and a signal peptide domain, indicating the enzymes are likely functional and exported to the extracellular environment where endo-chitinases usually act. Phylogenetic analysis revealed clade-specific diversification of endo-chitinases across the family. The presence of multiple, distinct endo-chitinases on the genomes of several Endozoicomonadaceae species hints at functional variation to secure effective chitin processing in diverse micro-niches and changing environmental conditions. We demonstrate that endo-chitinases and other genes involved in chitin degradation are widespread in the Endozoicomonadaceae family and posit that these symbionts play important roles in chitin turnover in filter- and suspension-feeding animals and in benthic, marine ecosystems at large.

Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of "replacement" through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles.

Chitinases as key virulence factors in microbial pathogens: Understanding their role and potential as therapeutic targets

Chitinases are crucial for the survival of bacterial and fungal pathogens both during host infection and outside the host in the environment. Chitinases facilitate adhesion onto host cells, act as virulence factors during infection, and provide protection from the host immune system, making them crucial factors in the survival of microbial pathogens. Understanding the mechanisms behind chitinase action is beneficial to design novel therapeutics to control microbial infections. This review explores the role of chitinases in the pathogenesis of bacterial, fungal, and viral infections. The mechanisms underlying the action of chitinases of bacterial, fungal, and viral pathogens in host cells are thoroughly reviewed. The evolutionary relationships between chitinases of various bacterial, fungal, and viral pathogens are discussed to determine their involvement in processes, such as adhesion and host immune system modulation. Gaining a better understanding of the distribution and activity of chitinases in these microbial pathogens can help elucidate their role in the invasion and infection of host cells.

Dual-Pulsed Laser Ablation of Oyster Shell Producing Novel Thin Layers Deposed to Saccharomyces cerevisiae

Dual-pulsed (DPL) laser deposition using oyster shells as targets was studied in order to find out if this method can replace the use of high-power pulsed lasers. Aspects related to changes in the morphological structure of the thin layer but also to the chemical composition of the obtained thin layer were analyzed and compared with the target as well as with the thin layers obtained with a higher power pulsed laser in a single-pulsed (SPL) regime. Orthorhombic structures were noticed with Scanning Electron Microscopy for the thin film obtained in DPL mode compared to the irregular particles obtained in SPL mode. The deacetylation process during ablation was evidenced by Fourier Transform Infrared spectroscopy, resulting in chitosan-based thin films. The effect of the obtained thin films of chitosan on the cells of baker's yeast (Saccharomyces cerevisiae) was studied. Restoration of the yeast paste into initial yeast was noticed mainly when the hemp fabric was used as support for the coating with yeas which was after that coated with chitosan thin film produced by DPL method.

The effects of differential feeding on ileum development, digestive ability and health status of newborn calves

Pre-weaning is the most important period for the growth and development of calves. Intestinal morphology, microbial community and immunity are initially constructed at this stage, and even have a lifelong impact on calves. Early feeding patterns have a significant impact on gastrointestinal development and microbial communities. This study mainly analyzed the effects of three feeding methods on the gastrointestinal development of calves, and provided a theoretical basis for further improving the feeding mode of calves. it is very important to develop a suitable feeding mode. In this study, we selected nine newborn healthy Holstein bull calves were randomly selected and divided into three groups (n = 3), which were fed with starter + hay + milk (SH group), starter + milk (SF group), total mixed ration + milk (TMR group). After 80 days of feeding Feeding to 80 days of age after, the ileum contents and blood samples were collected, and the differences were compared and analyzed by metagenomic analysis and serum metabolomics analysis. Results show that compared with the other two groups, the intestinal epithelium of the SH group was more complete and the goblet cells developed better. The feeding method of SH group was more conducive to the development of calves, with higher daily gain and no pathological inflammatory reaction. The intestinal microbial community was more conducive to digestion and absorption, and the immunity was stronger. These findings are helpful for us to explore better calf feeding patterns. In the next step, we will set up more biological replicates to study the deep-seated reasons for the differences in the development of pre-weaning calves. At the same time, the new discoveries of neuro microbiology broaden our horizons and are the focus of our future attention.

Unleashing the Potential of Bacterial Isolates from Apple Tree Rhizosphere for Biocontrol of Monilinia laxa: A Promising Approach for Combatting Brown Rot Disease

Monilinia laxa, a notorious fungal pathogen responsible for the devastating brown rot disease afflicting apples, wreaks havoc in both orchards and storage facilities, precipitating substantial economic losses. Currently, chemical methods represent the primary means of controlling this pathogen in warehouses. However, this study sought to explore an alternative approach by harnessing the biocontrol potential of bacterial isolates against brown rot in apple trees. A total of 72 bacterial isolates were successfully obtained from the apple tree rhizosphere and subjected to initial screening via co-cultivation with the pathogen. Notably, eight bacterial isolates demonstrated remarkable efficacy, reducing the mycelial growth of the pathogen from 68.75 to 9.25%. These isolates were subsequently characterized based on phenotypic traits, biochemical properties, and 16S rRNA gene amplification. Furthermore, we investigated these isolates' production capacity with respect to two enzymes, namely, protease and chitinase, and evaluated their efficacy in disease control. Through phenotypic, biochemical, and 16S rRNA gene-sequencing analyses, the bacterial isolates were identified as Serratia marcescens, Bacillus cereus, Bacillus sp., Staphylococcus succinus, and Pseudomonas baetica. In dual culture assays incorporating M. laxa, S. marcescens and S. succinus exhibited the most potent degree of mycelial growth inhibition, achieving 68.75 and 9.25% reductions, respectively. All the bacterial isolates displayed significant chitinase and protease activities. Quantitative assessment of chitinase activity revealed the highest levels in strains AP5 and AP13, with values of 1.47 and 1.36 U/mL, respectively. Similarly, AP13 and AP6 exhibited the highest protease activity, with maximal enzyme production levels reaching 1.3 and 1.2 U/mL, respectively. In apple disease control assays, S. marcescens and S. succinus strains exhibited disease severity values of 12.34% and 61.66% (DS), respectively, highlighting their contrasting efficacy in mitigating disease infecting apple fruits. These findings underscore the immense potential of the selected bacterial strains with regard to serving as biocontrol agents for combatting brown rot disease in apple trees, thus paving the way for sustainable and eco-friendly alternatives to chemical interventions.

Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species

Chitin is the second most abundant polysaccharide worldwide as part of arthropods' exoskeletons and fungal cell walls. Low concentrations in soils and sediments indicate rapid decomposition through chitinolytic organisms in terrestrial and aquatic ecosystems. The enacting enzymes, so-called chitinases, and their products, chitooligosaccharides, exhibit promising characteristics with applications ranging from crop protection to cosmetics, medical, textile, and wastewater industries. Exploring novel chitinolytic organisms is crucial to expand the enzymatical toolkit for biotechnological chitin utilization and to deepen our understanding of diverse catalytic mechanisms. In this study, we present two long-read sequencing-based genomes of highly similar Jeongeupia species, which have been screened, isolated, and biochemically characterized from chitin-amended soil samples. Through metabolic characterization, whole-genome alignments, and phylogenetic analysis, we could demonstrate how the investigated strains differ from the taxonomically closest strain Jeongeupia naejangsanensis BIO-TAS4-2T (DSM 24253). In silico analysis and sequence alignment revealed a multitude of highly conserved chitinolytic enzymes in the investigated Jeongeupia genomes. Based on these results, we suggest that the two strains represent a novel species within the genus of Jeongeupia, which may be useful for environmentally friendly N-acetylglucosamine production from crustacean shell or fungal biomass waste or as a crop protection agent.

An insight on sources and biodegradation of bioplastics: a review

Durability and affordability are two main reasons for the widespread consumption of plastic in the world. However, the inability of these materials to undergo degradation has become a significant threat to the environment and human health To address this issue, bioplastics have emerged as a promising alternative. Bioplastics are obtained from renewable and sustainable biomass and have a lower carbon footprint and emit fewer greenhouse gases than petroleum-based plastics. The use of these bioplastics sourced from renewable biomass can also reduce the dependency on fossil fuels, which are limited in availability. This review provides an elaborate comparison of biodegradation rates of potential bioplastics in soil from various sources such as biomass, microorganisms, and monomers. These bioplastics show great potential as a replacement for conventional plastics due to their biodegradable and diverse properties.

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Enhancing Rearing of European Seabass (Dicentrarchus labrax) in Aquaponic Systems: Investigating the Effects of Enriched Black Soldier Fly (Hermetia illucens) Prepupae Meal on Fish Welfare and Quality Traits

Within the modern aquaculture goals, the present study aimed to couple sustainable aquafeed formulation and culturing systems. Two experimental diets characterized by 3 and 20% of fish meal replacement with full-fat spirulina-enriched black soldier fly (Hermetia illucens) prepupae meal (HPM3 and HPM20, respectively) were tested on European seabass (Dicentrarchus labrax) juveniles during a 90-day feeding trial performed in aquaponic systems. The experimental diets ensured 100% survival and proper zootechnical performance. No behavioral alterations were evidenced in fish. Histological and molecular analyses did not reveal structural alterations and signs of inflammation at the intestinal level, highlighting the beneficial role on gut health of bioactive molecules typical of HPM or derived from the enriching procedure of insects' growth substrate with spirulina. Considering the quality traits, the tested experimental diets did not negatively alter the fillet's fatty acid profile and did not compromise the fillet's physical features. In addition, the results highlighted a possible role of spirulina-enriched HPM in preserving the fillet from lipid oxidation. Taken together, these results corroborate the use of sustainable ingredients (spirulina-enriched HPM) in aquaponic systems for euryhaline fish rearing.

Bioconversion of chitin into chitin oligosaccharides using a novel chitinase with high chitin-binding capacity

Chitin is the second largest renewable biomass resource in nature, it can be enzymatically degraded into high-value chitin oligosaccharides (CHOSs) by chitinases. In this study, a chitinase (ChiC8-1) was purified and biochemically characterized, its structure was analyzed by molecular modeling. ChiC8-1 had a molecular mass of approximately 96 kDa, exhibited its optimal activity at pH 6.0 and 50 °C. The K_m and V_max values of ChiC8-1 towards colloidal chitin were 10.17 mg mL^-1 and 13.32 U/mg, respectively. Notably, ChiC8-1 showed high chitin-binding capacity, which may be related to the two chitin binding domains in the N-terminal. Based on the unique properties of ChiC8-1, a modified affinity chromatography method, which combines protein purification with chitin hydrolysis process, was developed to purify ChiC8-1 while hydrolyzing chitin. In this way, 9.36 ± 0.18 g CHOSs powder was directly obtained by hydrolyzing 10 g colloidal chitin with crude enzyme solution. The CHOSs were composed of 14.77-2.83 % GlcNAc and 85.23-97.17 % (GlcNAc)₂ at different enzyme-substrate ratio. This process simplifies the tedious purification and separation steps, and may enable its potential application in the field of green production of chitin oligosaccharides.

Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar)

Chitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered "nonchitinous" organisms, despite having highly conserved chitin metabolism-associated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet, little is known about the genes and proteins responsible for these dynamic processes. Here, we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin metabolism in teleosts, with a particular focus on Atlantic salmon. Reconstruction of gene family phylogenies provides evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). The findings presented here support the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier.

Long-term nitrogen fertilization-induced enhancements of acid hydrolyzable nitrogen are mainly regulated by the most vital microbial taxa of keystone species and enzyme activities

It is well known that nitrogen (N) fertilizer input is required to improve crop productivity, but we lack a comprehensive understanding of how elevated N input changes the formation of soil acid hydrolyzable nitrogen (AHN) by adjusting the most vital microbial taxa of keystone species of microbial communities and enzyme activities. A 15-year field experiment comprising four levels of inorganic N fertilization was conducted to identify the most important bacterial and fungal taxa of the keystone species derived from cooccurrence networks as well as the vital enzyme activities at the bell mouth and maturity stages. Long-term N fertilization significantly increased the levels of AHN along with its four fractions, including amino acid N (AAN), ammonium N (AN), amino sugar N (ASN), and hydrolysable unidentified N (HUN), by 30.1-118.6 %, regardless of growth stage. Some most vital microbial taxa of keystone species and enzyme activities, which changed in response to N fertilization, mainly regulated each ANH fraction, that is, AHN and AN were mainly controlled by the enrichment of Nocardioides and β-1,4-N-acetyl-glucosaminidase (NAG), as well as by the reduction of Anaerolinea and urease (UR), AAN was determined by the enrichment of Hannaella and depletion of Penicillium, ASN was regulated by the enrichment of Hannaella and Arthrobacter, and HUN was influenced by the reduction of Penicillium and enrichment of Nitrosospira. These microbial genera have been found to be involved in dissimilatory nitrate reduction to ammonium (DNRA) and nitrification/denitrification processes and the two enzyme activities involved in organic N degradation and N-releasing processes, suggesting that the formation of AHN fractions was closely associated with specific functional microbial taxa and enzyme activities induced by N fertilization. Our results provide new insights into the associations among increased N input, altered formation of soil organic N, and shifts in microbial communities and enzyme activities.

Shell disease syndromes of decapod crustaceans

The term shell disease subsumes a number of debilitating conditions affecting the outer integument (the carapace) of decapod crustaceans, such as lobsters and crabs. Herein, we seek to find commonality in the aetiology and pathology of such conditions, and those cases that result in the progressive erosion of the cuticle through to the visceral tissues by a cocktail of microbial-derived enzymes including lipases, proteases and chitinases. Aquimarina spp. are involved in shell disease in many different crustaceans across a wide geographical area, but the overall view is that the condition is polymicrobial in nature leading to dysbiosis within the microbial consortium of the damaged cuticle. The role of environment, decapod behaviour and physiology in triggering this disease is also reviewed. Finally, we provide a conceptual model for disease aetiology and suggest several avenues for future research that could improve our understanding of how such factors trigger, or exacerbate, this condition.

The synergistic action of two chitinases from Vibrio harveyi on chitin degradation

In this study, two chitinases (VhChit2 and VhChit6) from Vibrio harveyi possessed specific activity of 36.5 and 20.8 U/mg, respectively. Structure analysis indicates that their amino acid composition of active sites is similar, but the substrate binding cleft of VhChit2 is deeper than that of VhChit6. They were shown to have a synergistic effect on chitin degradation, and the optimized degree of synergy and the degradation ratio of chitin reached 1.75 and 23.6 %, respectively. The saturated adsorption capacity of VhChit2 and VhChit6 adsorbed in 1 g of chitin was 48.5 and 33.4 mg. It was found that VhChit2 and VhChit6 had different adsorption sites on chitin, making more enzymes absorbed by chitin. Furthermore, the combined use of VhChit2 and VhChit6 increased their binding force of chitinases with the substrate. The synergistic action of VhChit2 and VhChit6 may be attributed to their different adsorption sites on chitin and the increased binding force with chitin.

Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions

The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO₂, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.

Microbial Exopolysaccharide Composites in Biomedicine and Healthcare: Trends and Advances

Microbial exopolysaccharides (EPSs), e.g., xanthan, dextran, gellan, curdlan, etc., have significant applications in several industries (pharma, food, textiles, petroleum, etc.) due to their biocompatibility, nontoxicity, and functional characteristics. However, biodegradability, poor cell adhesion, mineralization, and lower enzyme activity are some other factors that might hinder commercial applications in healthcare practices. Some EPSs lack biological activities that make them prone to degradation in ex vivo, as well as in vivo environments. The blending of EPSs with other natural and synthetic polymers can improve the structural, functional, and physiological characteristics, and make the composites suitable for a diverse range of applications. In comparison to EPS, composites have more mechanical strength, porosity, and stress-bearing capacity, along with a higher cell adhesion rate, and mineralization that is required for tissue engineering. Composites have a better possibility for biomedical and healthcare applications and are used for 2D and 3D scaffold fabrication, drug carrying and delivery, wound healing, tissue regeneration, and engineering. However, the commercialization of these products still needs in-depth research, considering commercial aspects such as stability within ex vivo and in vivo environments, the presence of biological fluids and enzymes, degradation profile, and interaction within living systems. The opportunities and potential applications are diverse, but more elaborative research is needed to address the challenges. In the current article, efforts have been made to summarize the recent advancements in applications of exopolysaccharide composites with natural and synthetic components, with special consideration of pharma and healthcare applications.

Persistence of a Wild-Type Virulent Aeromonas hydrophila Isolate in Pond Sediments from Commercial Catfish Ponds: A Laboratory Study

Virulent Aeromonas hydrophila (vAh) is a major bacterial pathogen in the U.S. catfish industry and is responsible for large-scale losses within commercial ponds. Administering antibiotic feeds can effectively treat vAh infections, but it is imperative to discern new approaches and better understand the mechanics of infection for this bacterium. As such, the persistence of vAh in pond sediments was determined by conducting laboratory trials using sediment from four commercial catfish ponds. Twelve chambers contained sterilized sediment, vAh isolate ML-09-119, and 8 L of water maintained at 28 °C and were aerated daily. At 1, 2, 4, 6, and 8 days, and every 7th day post-inoculation for 28 days, 1 g of sediment was removed, and vAh colony forming units (CFU) were enumerated on ampicillin dextrin agar. Viable vAh colonies were present in all sediments at all sampling periods. The vAh growth curve peaked (1.33 ± 0.26 × 10⁹ CFU g^-1) at 96 h post-inoculation. The population plateaued between days 14 and 28. No correlations were found between CFU g^-1 and physiochemical sediment variables. This study validated the ability of vAh to persist within pond sediments in a laboratory setting. Further research on environmental factors influencing vAh survivability and population dynamics in ponds is needed.

Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland

Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.

Habitat complexity affects microbial growth in fractal maze

The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.

Determinants of synergistic cell-cell interactions in bacteria

Bacteria are ubiquitous and colonize virtually every conceivable habitat on earth. To achieve this, bacteria require different metabolites and biochemical capabilities. Rather than trying to produce all of the needed materials by themselves, bacteria have evolved a range of synergistic interactions, in which they exchange different commodities with other members of their local community. While it is widely acknowledged that synergistic interactions are key to the ecology of both individual bacteria and entire microbial communities, the factors determining their establishment remain poorly understood. Here we provide a comprehensive overview over our current knowledge on the determinants of positive cell-cell interactions among bacteria. Taking a holistic approach, we review the literature on the molecular mechanisms bacteria use to transfer commodities between bacterial cells and discuss to which extent these mechanisms favour or constrain the successful establishment of synergistic cell-cell interactions. In addition, we analyse how these different processes affect the specificity among interaction partners. By drawing together evidence from different disciplines that study the focal question on different levels of organisation, this work not only summarizes the state of the art in this exciting field of research, but also identifies new avenues for future research.

Adaptive genetic traits in pelagic freshwater microbes

Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.

Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community

Microbial communities thrive in almost all habitats on earth. Within these communities, cells interact through the release and uptake of metabolites. These interactions can have synergistic or antagonistic effects on individual community members. The collective metabolic activity of microbial communities leads to changes in their local environment. As the environment changes over time, the nature of the interactions between cells can change. We currently lack understanding of how such dynamic feedbacks affect the growth dynamics of individual microbes and of the community as a whole. Here we study how interactions mediated by the exchange of metabolites through the environment change over time within a simple marine microbial community. We used a microfluidic-based approach that allows us to disentangle the effect cells have on their environment from how they respond to their environment. We found that the interactions between two species-a degrader of chitin and a cross-feeder that consumes metabolic by-products-changes dynamically over time as cells modify their environment. Cells initially interact positively and then start to compete at later stages of growth. Our results demonstrate that interactions between microorganisms are not static and depend on the state of the environment, emphasizing the importance of disentangling how modifications of the environment affects species interactions. This experimental approach can shed new light on how interspecies interactions scale up to community level processes in natural environments.

Environmental Reservoirs of Pathogenic Vibrio spp. and Their Role in Disease: The List Keeps Expanding

Vibrio species are natural inhabitants of aquatic environments and have complex interactions with the environment that drive the evolution of traits contributing to their survival. These traits may also contribute to their ability to invade or colonize animal and human hosts. In this review, we attempt to summarize the relationships of Vibrio spp. with other organisms in the aquatic environment and discuss how these interactions could potentially impact colonization of animal and human hosts.

Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals

Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.

Microbial chitinases and their relevance in various industries

Chitin, the second most abundant biopolymer on earth after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) units. It is widely distributed in nature, especially as a structural polysaccharide in the cell walls of fungi, the exoskeletons of crustaceans, insects, and nematodes. However, the principal commercial source of chitin is the shells of marine or freshwater invertebrates. Microbial chitinases are largely responsible for chitin breakdown in nature, and they play an important role in the ecosystem's carbon and nitrogen balance. Several microbial chitinases have been characterized and are gaining prominence for their applications in various sectors. The current review focuses on chitinases of microbial origin, their diversity, and their characteristics. The applications of chitinases in several industries such as agriculture, food, the environment, and pharmaceutical sectors are also highlighted.