Biofilms and Coronavirus Reservoirs: a Perspective Review

Bats are a key reservoir of coronaviruses (CoVs), including the agent of the severe acute respiratory syndrome, SARS-CoV-2, responsible for the recent deadly viral pneumonia pandemic. However, understanding how bats can harbor several microorganisms without developing illnesses is still a matter under discussion. Viruses and other pathogens are often studied as stand-alone entities, despite that, in nature, they mostly live in multispecies associations called biofilms-both externally and within the host. Microorganisms in biofilms are enclosed by an extracellular matrix that confers protection and improves survival. Previous studies have shown that viruses can secondarily colonize preexisting biofilms, and viral biofilms have also been described. In this review, we raise the perspective that CoVs can persistently infect bats due to their association with biofilm structures. This phenomenon potentially provides an optimal environment for nonpathogenic and well-adapted viruses to interact with the host, as well as for viral recombination. Biofilms can also enhance virion viability in extracellular environments, such as on fomites and in aquatic sediments, allowing viral persistence and dissemination. Moreover, understanding the biofilm lifestyle of CoVs in reservoirs might contribute to explaining several burning questions as to persistence and transmissibility of highly pathogenic emerging CoVs.

Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.

Plant Growth-Promoting Rhizobacteria HN6 Induced the Change and Reorganization of Fusarium Microflora in the Rhizosphere of Banana Seedlings to Construct a Healthy Banana Microflora

Streptomyces aureoverticillatus HN6 was isolated in our previous study and effectively controlled banana Fusarium wilt. We explored the role of HN6 in constructing a healthy rhizosphere microflora of banana seedlings. The method of antibiotic resistance was used to determine the colonization ability of HN6. The effect of HN6 on the rhizosphere microbial communities was assessed using culture-dependent and high-throughput sequencing. The effect of HN6 on the infection process of the pathogen was evaluated using a pot experiment and confocal laser scanning microscopy. The results showed that HN6 could prevent pathogen infection; it increased the nutrient content and diversity of the bacterial community in the rhizosphere, promoted plant growth, and decreased the mycotoxin fusaric acid content and abundance of pathogens in the banana rhizosphere. Thus, HN6 decreased the relative abundance of Fusarium species, increased the diversity of fungi, and increased the relative abundance of bacteria in the rhizosphere. HN6 induced the change and reorganization of the microbial community dominated by Fusarium in the rhizosphere of banana seedlings, and it evolved into a community dominated that was not conducive to the occurrence of diseases, shaping the rhizosphere microflora and promoting the growth of banana.

Characterization of Binary Biofilms of Listeria monocytogenes and Lactobacillus and Their Response to Chlorine Treatment

In nature, Listeria may interact competitively and cooperatively with other organisms, resulting in unique spatial organization and functions for cells within the community. This study was undertaken to characterize the biofilm architecture of binary biofilms of Listeria monocytogenes and Lactobacillus species and to assess their effect on the survival of Listeria during exposure to hypochlorite. Three L. monocytogenes strains, ATCC 19115 (Lm5), ATCC 19117 (Lm7), and Coleslaw (LmC), were selected and combined individually with three Lactobacillus strains: L. fermentum (Lf), L. bavaricus (Lb), and L. plantarum (Lp). In binary Lm-Lp biofilms, the Lm cell counts were similar to single-species biofilms (8.5 log CFU/well), and the Lp cell numbers declined by 1.0 log CFU/well. In the presence of Lb, the Lm cell counts were reduced by 1.5 log CFU/well (p < 0.05), whereas the Lf cell counts increased at least by 3.5 log CFU/well. Confocal laser scanning microscopy (CLSM) determined that interspecies interactions significantly affected the spatial organization of three binary biofilms. Biofilm surface-to-volume ratio increased from 0.8 μm²/μm³ for Lm5 in the monoculture to 2.1 μm²/μm³ for Lm5-Lp in the dual-species model (p < 0.05), and was characterized by a thicker structure with a largely increased surface area. Biofilm roughness increased from 0.2 for Lm7 to 1.0 for Lm7-Lb biofilms (p < 0.05), which appeared as interspecific segregation. Biofilm thickness increased from 34.2 μm for LmC to 46.3 μm for LmC–Lf (p < 0.05), which produced flat and compact structures that covered the entire surface available. The biomass of the extracellular matrix was higher in the case of some binary biofilms (p < 0.05); however, this effect was dependent upon the species pair. When treated with hypochlorite, Lm5 in binary biofilms had an approximately 1.5 log CFU/well greater survival than individually. The unique spatial organization and greater protein production may explain the protective effect of Lp after hypochlorite exposure.

Tissue Type: A Crucial Factor Influencing the Fungal Diversity and Communities in Sichuan Pork Bacon

This study aimed to the variations of fungal diversity and community structure in different parts of traditional homemade Sichuan pork bacon. A total of seven phyla and 91 fungal genera were identified. Among them, Ascomycota and Basidiomycota were the first and second most abundant phyla in the bacon tissues. In addition, five dominant genera (Aspergillus, Candida, Debaryomyces, Malassezia, and Penicillium) were shared by all bacon tissues. The numbers of OTUs unique to individual groups were 14, 67, and 65 for the muscle tissue, the adipose tissue, and pork skin, respectively. Linear discriminant analysis showed that a total of 31 taxa significantly differed among the groups. Results of redundancy analysis indicated that fat content, protein content, aw, and pH of bacon tissue shaped the bacon fungal communities. Results of network analysis also indicated that tissue type was a crucial factor influencing the fungal interactions in different tissues. This study can lay a foundation for further isolation and identification of fungi in the product and provides a basis for further research of food health in homemade traditional pork bacon.

Microbiome Analysis Reveals Microecological Balance in the Emerging Rice-Crayfish Integrated Breeding Mode

The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.

Biocontrol Agents: Toolbox for the Screening of Weapons against Mycotoxigenic Fusarium

The aim of this study was to develop a set of experiments to screen and decipher the mechanisms of biocontrol agents (BCAs), isolated from commercial formulation, against two major mycotoxigenic fungi in cereals, Fusarium graminearum and Fusarium verticillioides. These two phytopathogens produce mycotoxins harmful to human and animal health and are responsible for the massive use of pesticides, for the protection of cereals. It is therefore essential to better understand the mechanisms of action of alternative control strategies such as the use of BCAs in order to optimize their applications. The early and late stages of interaction between BCAs and pathogens were investigated from germination of spores to the effects on perithecia (survival form of pathogen). The analysis of antagonist activities of BCAs revealed different strategies of biocontrol where chronological, process combination and specialization aspects of interactions are discussed. Streptomyces griseoviridis main strategy is based on antibiosis with the secretion of several compounds with anti-fungal and anti-germination activity, but also a mixture of hydrolytic enzymes to attack pathogens, which compensates for an important deficit in terms of spatial colonization capacity. It has good abilities in terms of nutritional competition. Trichoderma asperellum is capable of activating a very wide range of defenses and attacks combining the synthesis of various antifungal compounds (metabolite, enzymes, VOCs), with different targets (spores, mycelium, mycotoxins), and direct action by mycoparasitism and mycophagy. Concerning Pythium oligandrum, its efficiency is mainly due to its strong capacity to colonize the environment, with a direct action via microbial predation, stimulation of its reproduction at the contact of pathogens and the reduction of perithecia formation.

Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation

Rhizobacteria live in diverse and dynamic communities having a high impact on plant growth and development. Due to the complexity of the microbial communities and the difficult accessibility of the rhizosphere, investigations of interactive processes within this bacterial network are challenging. In order to better understand causal relationships between individual members of the microbial community of plants, we started to investigate the inter- and intraspecific interaction potential of three rhizobacteria, the S. plymuthica isolates 4Rx13 and AS9 and B. subtilis B2g, using high resolution mass spectrometry based metabolic profiling of structured, low-diversity model communities. We found that by metabolic profiling we are able to detect metabolite changes during cultivation of all three isolates. The metabolic profile of S. plymuthica 4Rx13 differs interspecifically to B. subtilis B2g and surprisingly intraspecifically to S. plymuthica AS9. Thereby, the release of different secondary metabolites represents one contributing factor of inter- and intraspecific variations in metabolite profiles. Interspecific co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g showed consistently distinct metabolic profiles compared to mono-cultivated species. Thereby, putative known and new variants of the plipastatin family are increased in the co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g. Interestingly, intraspecific co-cultivation of S. plymuthica 4Rx13 and S. plymuthica AS9 revealed a distinct interaction zone and showed distinct metabolic profiles compared to mono-cultures. Thereby, several putative short proline-containing peptides are increased in co-cultivation of S. plymuthica 4Rx13 with S. plymuthica AS9 compared to mono-cultivated strains. Our results demonstrate that the release of metabolites by rhizobacteria alters due to growth and induced by social interactions between single members of the microbial community. These results form a basis to elucidate the functional role of such interaction-triggered compounds in establishment and maintenance of microbial communities and can be applied under natural and more realistic conditions, since rhizobacteria also interact with the plant itself and many other members of plant and soil microbiota.

Effect of Lactic Acid Bacteria Strains on the Growth and Aflatoxin Production Potential of Aspergillus parasiticus, and Their Ability to Bind Aflatoxin B1, Ochratoxin A, and Zearalenone in vitro

The increased consumption of plant-based foods has intensified the concern related to mycotoxin intoxication. This study aimed to investigate the effect of selected lactic acid bacteria (LAB) strains on the growth of Aspergillus parasiticus NRRL 2999 and its production of aflatoxin (AF). The ability of the heat-killed (100°C for 1 h) LAB strains to bind aflatoxin M₁ (AFM₁) in milk and aflatoxin B₁ (AFB₁), ochratoxin A (OTA), and zearalenone (ZEN) in potassium phosphate buffer (PPB) was also evaluated in vitro. Ten LAB strains were tested individually, by inoculating them simultaneously with the fungus or after incubation of the fungus for 24 or 48 h at 25°C. Double layer yeast extract sucrose (YES) agar, de Man Rogosa and Sharpe (MRS) agar, and YES broth were incubated for 7 days at 25°C to follow the development of the fungus. Levilactobacillus spp. 3QB398 and Levilactobacillus brevis 2QB422 strains were able to delay the growth of A. parasiticus in YES broth, even when these strains were inoculated 24 h after the fungus. The inhibitory effect of these LAB strains was confirmed by the reduction of fungus colony size, suggesting dominance of LAB by competition (a Lotka-Voltera effect). The production of AFB₁ by A. parasiticus was inhibited when the fungus was inoculated simultaneously with Lactiplantibacillus plantarum 3QB361 or L. plantarum 3QB350. No AFB₁ was found when Levilactobacillus spp. 2QB383 was present, even when the LAB was inoculated 48 h after the fungus. In binding studies, seven inactivated LAB strains were able to promote a reduction of at least 50% the level of AFB₁, OTA, and ZEN. This reduction varied depending on the pH of the PPB. In milk, however, only two inactivated LAB strains were able to reduce AFM₁, with a reduction of 33 and 45% for Levilactobacillus spp. 3QB398 (Levilactobacillus spp.) and L. brevis 2QB422, respectively. Nevertheless, these results clearly indicate the potential of using LAB for mycotoxin reduction.

Pseudomonas aeruginosa Virulence Factors Support Voriconazole Effects on Aspergillus fumigatus

Pseudomonas aeruginosa and Aspergillus fumigatus are pathogens that are associated with deterioration of lung function, e.g., in persons with cystic fibrosis (CF). There is evidence that co-infections with these pathogens cause airway inflammation and aggravate pathology in CF lungs. Intermicrobial competition of P. aeruginosa and A. fumigatus has been described, but it is unknown how anti-fungal therapy is affected. The anti-fungal azole voriconazole (VCZ), supernatants of P. aeruginosa laboratory isolates PA14 or PAO1, or clinical isolate Pa10 independently inhibited biofilm metabolism of A. fumigatus isolates 10AF and AF13073. When VCZ and supernatants were combined at their IC₅₀s, synergistic effects on A. fumigatus were found. Synergistic effects were no longer observed when P. aeruginosa supernatants were prepared in the presence of iron, or when P. aeruginosa mutants were lacking the ability to produce pyoverdine and pyochelin. Combination of pure P. aeruginosa products pyoverdine, pyochelin, and pyocyanin with VCZ showed synergistic anti-fungal effects. Combining VCZ with P. aeruginosa supernatants also improved its MIC and MFC against planktonic A. fumigatus. In summary, in the case of P. aeruginosa–A. fumigatus co-infections, it appeared that the P. aeruginosa co-infection facilitated therapy of the Aspergillus; lower concentrations of VCZ might be sufficient to control fungal growth.

Growth interferences between bacterial strains from raw cow's milk and their impact on growth of Listeria monocytogenes and Staphylococcus aureus

AIMS

The purpose of this study was to detect growth enhancing or inhibiting activity between bacterial populations from raw milk under different conditions (temperature, medium).

METHODS AND RESULTS

The interference of 24 raw milk isolates on growth of each other and on Listeria monocytogenes, Staphylococcus aureus, Bacillus subtilis and Micrococcus luteus was screened by drop assay and for selected pairs in co-cultivation experiments. By drop assay, antibacterial activity was observed for 40% of the strains. About 30% of the strains showed growth-enhancing activity on other strains. Most of the isolates were well adapted to cold temperatures and showed consistent or even increased inhibiting or enhancing effects on growth of other strains at 10°C. The growth of L. monocytogenes DSM 20600^T and S. aureus DSM 1104^T was significantly (P < 0·05) reduced in co-cultivation with Pseudomonas protegens JZ R-192.

CONCLUSIONS

Growth interferences between bacterial populations have an impact on the structure of raw milk microbiota, especially when it develops under cold storage, and it may have an effect on the prevalence of certain foodborne pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates growth-inhibiting and also growth-enhancing interactions between raw milk bacteria, which must be considered when predicting bacterial growth and spoilage in food. A Ps. protegens strain isolated from raw milk showed an antagonistic effect on growth of L. monocytogenes in refrigerated raw milk.

Sensitivity of Molds From Spoiled Dairy Products Towards Bioprotective Lactic Acid Bacteria Cultures

Fungal spoilage of dairy products is a major concern due to food waste and economical losses, some fungal metabolites may furthermore have adverse effects on human health. The use of lactic acid bacteria (LAB) is emerging as a potential clean label alternative to chemical preservatives. Here, our aim was to characterize the growth potential at three storage temperatures (5, 16, and 25°C) of a panel of molds (four Mucor and nine Penicillium strains) isolated from dairy products, then investigate the susceptibility of the molds toward 12 LAB cultures. Fungal cell growth and morphology in malt extract broth was monitored using oCelloScope at 25°C for 24 h. Mucor plumbeus 01180036 was the fastest growing and Penicillium roqueforti ISI4 (P. roqueforti ISI4) the slowest of the tested molds. On yogurt-agar plates, all molds grew at 5, 16, and 25°C in a temperature-dependent manner with Mucor strains growing faster than Penicillium strains regardless of temperature. The sensitivity toward 12 LAB cultures was tested using high-throughput overlay method and here all the molds except P. roqueforti ISI4 were strongly inhibited. The antifungal action of these LAB was confirmed when spotting mold spores on agar plates containing live cells of the LAB strains. However, if cells were removed from the fermentates, the inhibitory effects decreased markedly. The antifungal effects of volatiles tested in a plate-on-plate system without direct contact between mold and LAB culture media were modest. Some LAB binary combinations improved the antifungal activity against the growth of several molds beyond that of single cultures in yogurt serum. The role of competitive exclusion due to manganese depletion was examined as a possible antifungal mechanism for six Penicillium and two Mucor strains. It was shown that this mechanism was a major inhibition factor for the molds tested apart from the non-inhibited P. roqueforti ISI4 since addition of manganese with increasing concentrations of up to 0.1 mM resulted in partly or fully restored mold growth in yogurt. These findings help to understand the parameters influencing the mold spoilage of dairy products and the interactions between the contaminating strains, substrate, and bioprotective LAB cultures.

Omics-based microbiome analysis in microbial ecology: from sequences to information

Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.

Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs

Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, dynamics, and ecology of eukaryotic heterotrophs. Here, we focus on the Labyrinthulomycetes, a fungus-like protistan group whose biomass can exceed that of the bacterioplankton in coastal waters. We examined their diversity and community structure in a weekly temperate coastal ocean time series. Their seasonal community patterns were related to temperature, insolation, dissolved inorganic carbon, fungal abundance, ammonia, chlorophyll a, pH, and other environmental variables. Similar to the bacterioplankton, annual community patterns of the Labyrinthulomycetes were dominated by a few persistent taxa with summer or winter preferences. However, like the patterns of fungi at this site, the majority of the Labyrinthulomycetes phylotypes occurred mostly as short, reoccurring, season-specific blooms. Furthermore, some specific phylotypes of Labyrinthulomycetes displayed time-lagged correlations or cooccurrences with bacterial, algal, or fungal phylotypes, suggesting their potentially multifaceted involvement in the marine food webs. Overall, this study reports niche partitioning between closely related Labyrinthulomycetes and identifies distinct ecotypes and temporal patterns compared to bacterioplankton and fungi.IMPORTANCE Increasing evidence has shown that heterotrophic microeukaryotes are an important component in global marine ecosystems, while their diversity and ecological functions remain largely unknown. Without appropriately incorporating these organisms into the food web models, our current understanding of marine microbial community ecology is incomplete, which may further hamper broader studies of biogeochemistry and climate change. This study focuses on a major group of unicellular fungus-like protists (Labyrinthulomycetes) and reveals their distinct annual community patterns relative to fungi and bacteria. Results of our observations provide new information on the community structure and ecology of this protistan group and shed light on the intricate ecological roles of unicellular heterotrophic eukaryotes in the coastal oceans.

Updating changes in human gut microbial communities associated with Clostridioides difficile infection

Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, a worldwide public health problem. Different factors can promote the progression of C. difficile infection (CDI), mainly altered intestinal microbiota composition. Microbial species belonging to different domains (i.e., bacteria, archaea, eukaryotes, and even viruses) are synergistically and antagonistically associated with CDI. This review was aimed at updating changes regarding CDI-related human microbiota composition using recent data and an integral approach that included the different microorganism domains. The three domains of life contribute to intestinal microbiota homeostasis at different levels in which relationships among microorganisms could explain the wide range of clinical manifestations. A holistic understanding of intestinal ecosystem functioning will facilitate identifying new predictive factors for infection and developing better treatment and new diagnostic tools, thereby reducing this disease's morbidity and mortality.

Association Between Gut Akkermansia and Metabolic Syndrome is Dose-Dependent and Affected by Microbial Interactions: A Cross-Sectional Study

OBJECTIVE

Akkermansia muciniphila is among the most abundant bacterial species in the human intestine; however, its relationship to metabolic syndrome (MetS)-which is linked to gut dysbiosis-is not known. In this study, we investigated the association between Akkermansia abundance and risk of MetS and its components, as well as dose-response effects and the influence of microbial interactions on the association.

METHODS

This cross-sectional study included 6896 Chinese participants aged 18 to 97 years from the Guangdong Gut Microbiome Project. MetS was defined according to Joint Committee for Developing Chinese Guidelines on Prevention and Treatment of Dyslipidemia in Adults criteria. The abundance of Akkermansia was assessed by 16S rRNA sequencing. Logistic regression analysis with adjustment for common confounders was performed to evaluate the association between Akkermansia and MetS and its components. Models with restricted cubic splines and interaction terms were used to examine the dose-response association and microbial interactions, respectively.

RESULTS

The prevalence of MetS was 20.4%, and the median abundance of Akkermansia was 0.08% (interquartile range: 0.04-0.93%). Increased Akkermansia abundance was associated with decreased risk of MetS (P _nonlinear<0.05), but this effect was not observed until the Akkermansia level was 0.2% of the total gut microbiota abundance (odds ratio=0.96, 95% confidence interval: 0.94-0.98). Of the 5 MetS components, obesity and hypertriglyceridemia showed the strongest association with Akkermansia, followed by reduced high-density lipoprotein cholesterol, hypertension, and hyperglycemia. Microbial interaction analyses showed that Ruminococcaceae and Lachnospiraceae were the predominant bacterial families and were not only correlated with Akkermansia abundance but also influenced the Akkermansia-MetS association.

CONCLUSION

There is a dose-response association between reduced risk of MetS and increased abundance of Akkermansia. The association between Akkermansia and 5 MetS components is variable and affected by microbial interactions.

Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease

Major losses of crop yield and quality caused by soil-borne plant diseases have long threatened the ecology and economy of agriculture and forestry. Biological control using beneficial microorganisms has become more popular for management of soil-borne pathogens as an environmentally friendly method for protecting plants. Two major barriers limiting the disease-suppressive functions of biocontrol microbes are inadequate colonization of hosts and inefficient inhibition of soil-borne pathogen growth, due to biotic and abiotic factors acting in complex rhizosphere environments. Use of a consortium of microbial strains with disease inhibitory activity may improve the biocontrol efficacy of the disease-inhibiting microbes. The mechanisms of biological control are not fully understood. In this review, we focus on bacterial and fungal biocontrol agents to summarize the current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases. We discuss potential mechanisms used by microbial components to improve the disease suppressing efficacy. We emphasize the interaction-related factors to be considered when constructing multiple-strain biological control consortia and propose a workflow for assembling them by applying a reductionist synthetic community approach.

Effects of Antibiotic Treatment on Gut Microbiota and How to Overcome Its Negative Impacts on Human Health

The need for new antimicrobial therapies is evident, especially to reduce antimicrobial resistance and minimize deleterious effects on gut microbiota. However, although diverse studies discuss the adverse effects of broad-spectrum antibiotics on the microbiome ecology, targeted interventions that could solve this problem have often been overlooked. The impact of antibiotics on gut microbiota homeostasis is alarming, compromising its microbial community and leading to changes in host health. Recent studies have shown that these impacts can be transient or permanent, causing irreversible damage to gut microbiota. The responses to and changes in the gut microbial community arising from antibiotic treatment are related to its duration, the number of doses, antibiotic class, host age, genetic susceptibility, and lifestyle. In contrast, each individual's native microbiota can also affect the response to treatment as well as respond differently to antibiotic treatment. In this context, the current challenge is to promote the growth of potentially beneficial microorganisms and to reduce the proportion of microorganisms that cause dysbiosis, thus contributing to an improvement in the patient's health. An essential requirement for the development of novel antibiotics will be personalized medicinal strategies that recognize a patient's intestinal and biochemical individuality. Thus, this Review will address a new perspective on antimicrobial therapies through pathogen-selective antibiotics that minimize the impacts on human health due to changes in the gut microbiota from the use of antibiotics.

A study revealing volatile aroma produced by Pediococcus pentosaceus in dough fermentation

Pediococcus pentosaceus is important probiotics in Chinese Laomian. Its role in meat and fermented vegetable has been largely demonstrated, but few studies have investigated the role of P. pentosaceus in Chinese Laomian. For this purpose, we simulated Laomian fermentation using Saccharomyces cerevisiae and P. pentosaceus. Volatile aroma was detected by headspace solid-phase microextraction gas-chromatography-mass spectrometry. Real-time fluorescent quantitative polymerase chain reaction was used to determine dynamic growth of S. cerevisiae and P. pentosaceus in fermentation. Extracellular proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Folin-Ciocalteu method was used to detect extracellular protease activity in different pH values. Owing to addition of P. pentosaceus, the types and contents of esters increase, the relative contents of acetic acid hexyl ester, formic acid octyl ester, and heptanoic acid ethyl ester rise obliviously; especially, the relative content of hexanoic acid ethyl ester was highly correlated with P. pentosaceus by increasing 20.61%. As the gel electrophoresis results display, due to mixed fermentation of S. cerevisiae and P. pentosaceus, the 25k Da and 51k Da proteins expression quantity of P. pentosaceus clearly increased. Under neutral and alkaline culture conditions, the extracellular protease activity of P. pentosaceus is higher. This research benefits to gain insight into the fermentation actions of P. pentosaceus in Chinese Laomian.

Under nonlimiting iron conditions pyocyanin is a major antifungal molecule, and differences between prototypic Pseudomonas aeruginosa strains

Airways of immunocompromised patients, or individuals with cystic fibrosis (CF), are common ground for Pseudomonas aeruginosa and Aspergillus fumigatus infections. Hence, in such a microenvironment both pathogens compete for resources. While under limiting iron conditions the siderophore pyoverdine is the most effective antifungal P. aeruginosa product, we now provide evidence that under nonlimiting iron conditions P. aeruginosa supernatants lack pyoverdine but still possess considerable antifungal activity. Spectrometric analyses of P. aeruginosa supernatants revealed the presence of phenazines, such as pyocyanin, only under nonlimiting iron conditions. Supernatants of quorum sensing mutants of strain PA14, defective in phenazine production, as well as supernatants of the P. aeruginosa strain PAO1, lacked pyocyanin, and were less inhibitory toward A. fumigatus biofilms under nonlimiting iron conditions. When blood as a natural source of iron was present during P. aeruginosa supernatant production, pyoverdine was absent, and phenazines, including pyocyanin, appeared, resulting in an antifungal effect on A. fumigatus biofilms. Pure pyocyanin reduced A. fumigatus biofilm metabolism. In summary, P. aeruginosa has mechanisms to compete with A. fumigatus under limiting and non-limiting iron conditions, and can switch from iron-denial-based to toxin-based antifungal activity. This has implications for the evolution of the microbiome in clinical settings where the two pathogens co-exist. Important differences in the iron response of P. aeruginosa laboratory strains PA14 and PAO1 were also uncovered.

Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil

Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant–pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil.

Bacillus Responses to Plant-Associated Fungal and Bacterial Communities

Some members of root-associated Bacillus species have been developed as biocontrol agents due to their contribution to plant protection by directly interfering with the growth of pathogens or by stimulating systemic resistance in their host. As rhizosphere-dwelling bacteria, these bacilli are surrounded and constantly interacting with other microbes via different types of communications. With this review, we provide an updated vision of the molecular and phenotypic responses of Bacillus upon sensing other rhizosphere microorganisms and/or their metabolites. We illustrate how Bacillus spp. may react by modulating the production of secondary metabolites, such as cyclic lipopeptides or polyketides. On the other hand, some developmental processes, such as biofilm formation, motility, and sporulation may also be modified upon interaction, reflecting the adaptation of Bacillus multicellular communities to microbial competitors for preserving their ecological persistence. This review also points out the limited data available and a global lack of knowledge indicating that more research is needed in order to, not only better understand the ecology of bacilli in their natural soil niche, but also to better assess and improve their promising biocontrol potential.

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.