A robust plate assay for detection of extracellular microbial protease activity in metagenomic screens and pure cultures

Passive Droplet Microfluidic Platform for High-Throughput Screening of Microbial Proteolytic Activity

Traditional bacterial isolation methods are often costly, have limited throughput, and may not accurately reflect the true microbial community composition. Consequently, identifying rare or slow-growing taxa becomes challenging. Over the past decade, a new approach has been proposed to replace traditional flasks or multiwell plates with ultrahigh-throughput droplet microfluidic screening assays. In this study, we present a novel passive droplet-based method designed for isolating proteolytic microorganisms, which are crucial in various biotechnology industries. Following the encapsulation of single cells in gelatin microgel compartments and their subsequent clonal cultivation, microcultures are passively sorted at high throughput based on the deformability of droplets. Our novel chip design offers a 50-fold improvement in throughput compared to a previously developed deformability-based droplet sorter. This method expands an array of droplet-based microbial enrichment assays and significantly reduces the time and resources required to isolate proteolytic bacteria strains.

Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources

Ornate, large, extremophilic (OLE) RNAs comprise a class of large noncoding RNAs in bacteria whose members form a membrane-associated ribonucleoprotein (RNP) complex. This complex facilitates cellular adaptation to diverse stresses such as exposure to cold, short-chain alcohols, and elevated Mg2+ concentrations. Here, we report additional phenotypes exhibited by Halalkalibacterium halodurans (formerly called Bacillus halodurans) strains lacking functional OLE RNP complexes. Genetic disruption of the complex causes restricted growth compared to wild-type cells when cultured in minimal media (MM) wherein glucose is replaced with alternative carbon/energy sources. Genetic suppressor selections conducted in glutamate MM yielded isolates that carry mutations in or near genes relevant to Mn2+ homeostasis (ykoY and mntB), phosphate homeostasis (phoR), and putative multidrug resistance (bmrCD). These functional links between OLE RNA, carbon/energy management, and other fundamental processes including protein secretion are consistent with the hypothesis that the OLE RNP complex is a major contributor to cellular adaptation to unfavorable growth conditions.

TerC proteins function during protein secretion to metalate exoenzymes

Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.

Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans

Burkholderia multivorans is the dominant Burkholderia pathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study of B. multivorans was undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that the B. multivorans population separated into two distinct evolutionary clades, defined as lineage 1 (n=58 genomes) and lineage 2 (n=221 genomes). To examine the population biology of B. multivorans, a representative subgroup of 77 B. multivorans genomes (28 from the reference databases and the 49 novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identify B. multivorans lineage-specific genes - ghrB_1 in lineage 1 and glnM_2 in lineage 2 - and diagnostic PCRs targeting them were successfully developed. Phenotypic analysis of 49 representative B. multivorans strains showed considerable inter-strain variance, but the majority of the isolates tested were motile and capable of biofilm formation. A striking absence of B. multivorans protease activity in vitro was observed, but no lineage-specific phenotypic differences were demonstrated. Using phylogenomic and phenotypic criteria, three model B. multivorans CF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined. B. multivorans CF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies of B. multivorans.

TerC Proteins Function During Protein Secretion to Metalate Exoenzymes

Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn 2+ -dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn 2+ -dependent membrane and extracellular enzymes.

Alternaria alternata Isolated from Infected Pears (Pyrus communis) in Italy Produces Non-Host Toxins and Hydrolytic Enzymes as Infection Mechanisms and Exhibits Competitive Exclusion against Botrytis cinerea in Co-Infected Host Fruits

Alternaria alternata is one of the most devastating phytopathogenic fungi. This microorganism causes black spots in many fruits and vegetables worldwide, generating significant post-harvest losses. In this study, an A. alternata strain, isolated from infected pears (Pyrus communis) harvested in Italy, was characterized by focusing on its pathogenicity mechanisms and competitive exclusion in the presence of another pathogen, Botrytis cinerea. In in vitro assays, the fungus produces strong enzymatic activities such as amylase, xylanase, and cellulase, potentially involved during the infection. Moreover, it secretes four different toxins purified and identified as altertoxin I, alteichin, alternariol, and alternariol 4-methyl ether. Only alteichin generated necrotic lesions on host-variety pears, while all the compounds showed moderate to slight necrotic activity on non-host pears and other non-host fruit (lemon, Citrus limon), indicating they are non-host toxins. Interestingly, A. alternata has shown competitive exclusion to the competitor fungus Botrytis cinerea when co-inoculated in host and non-host pear fruits, inhibiting its growth by 70 and 65%, respectively, a result not observed in a preliminary characterization in a dual culture assay. Alteichin and alternariol 4-methyl ether tested against B. cinerea had the best inhibition activity, suggesting that the synergism of these toxins and enzymatic activities of A. alternata are probably involved in the competitive exclusion dynamics in host and non-host pear fruits.

Use of halotolerant Bacillus amyloliquefaciens RHF6 as a bio-based strategy for alleviating salinity stress in Lotus japonicus cv Gifu

Halotolerant (HT) bacteria are a group of microorganisms able to thrive in environments with relatively high salt concentrations. HT-microorganisms with plant growth-promoting (PGP) characteristics have been proposed to increase plant tolerance in salty soil. Here, we evaluated the PGP properties at increasing NaCl concentrations of HT-Bacillus strains, previously shown to have beneficial effects under physiological conditions. Most of the isolated showed indole acetic acid and ammonia production and were able to solubilize phosphate and suppress the proliferation of the phytopathogenic fungus Macrophomina phaseolina 2013-1 at high salt concentrations. One of the selected strains, Bacillus amyloliquefaciens RHF6, which retained its beneficial properties up to 400 mM NaCl in vitro, was tested on the legume model plant Lotus japonicus cv Gifu under salt stress. The inoculation with RHF6 significantly improved the survival of plants under high salinity conditions, as reflected in seedling root and shoot growth and total fresh weight (increased by 40%) when compared with non-inoculated plants. The ability of RHF6 to induce a plant antioxidant response, secrete the osmoprotectant proline and reduce ethylene level via the enzymatic ACC deaminase activity indicated this strain as a potentially helpful PGPB for the treatment of degraded soils.

An observational investigation of the faical microbiota and metabonome of gastrostomy fed children, on blended and formula diets

Gastrostomy fed children traditionally have a Formulae diet (FD), which fulfills nutritional requirements; however, many families are adopting Blended diets (BD), which are what the whole family would eat. We undertook an observational investigation of the colonic microbiota and metabonome in a small group of gastrostomy fed children, who were either on an FD or BD, and compared, where possible to their siblings (17 FD, 28 BD, 19 HS). There was no increase in complications in tube blockage or infection rates, but a significant improvement in the prevalence of bowel problems, a reduction in medication and an increase in quality of life. Metataxonomic analysis showed that the FD group was significantly different to the Sibling group, and that families did not cluster together. Whole sample metabonomics showed no differences between groups; however, univariate analysis of biologically important metabolites did differ. Changing to a BD resulted in no increase in complications or risks, but improved the overall quality of life for the children and families.

Plant Growth-Promoting Bacterial Consortia as a Strategy to Alleviate Drought Stress in Spinacia oleracea

Drought stress is one of the most severe abiotic stresses affecting soil fertility and plant health, and due to climate change, it is destined to increase even further, becoming a serious threat to crop production. An efficient, eco-friendly alternative is the use of plant growth-promoting bacteria (PGPB), which can promote plant fitness through direct and indirect approaches, protecting plants from biotic and abiotic stresses. The present study aims to identify bacterial consortia to promote Spinacia oleracea L. cv Matador’s seed germination and protect its seedlings from drought stress. Eight PGPB strains belonging to the Bacillus, Azotobacter, and Pseudomonas genera, previously characterized in physiological conditions, were analyzed under water-shortage conditions, and a germination bioassay was carried out by biopriming S. oleracea seeds with either individual strains or consortia. The consortia of B. amyloliquefaciens RHF6, B. amyloliquefaciens LMG9814, and B. sp. AGS84 displayed the capacity to positively affect seed germination and seedlings’ radical development in both standard and drought conditions, ameliorating the plants’ growth rate compared to the untreated ones. These results sustain using PGPB consortia as a valid ameliorating water stress strategy in the agro-industrial field.

Two-step functional screen on multiple proteinaceous substrates reveals temperature-robust proteases with a broad-substrate range

Abstract

To support the bio-based industry in development of environment-friendly processes and products, an optimal toolbox of biocatalysts is key. Although functional screen of (meta)genomic libraries may potentially contribute to identifying new enzymes, the discovery of new enzymes meeting industry compliance demands is still challenging. This is particularly noticeable in the case of proteases, for which the reports of metagenome-derived proteases with industrial applicability are surprisingly limited. Indeed, proteolytic clones have been typically assessed by its sole activity on casein or skim milk and limited to mild screening conditions. Here, we demonstrate the use of six industry-relevant animal and plant by-products, namely bone, feather, blood meals, gelatin, gluten, and zein, as complementary substrates in functional screens and show the utility of temperature as a screening parameter to potentially discover new broad-substrate range and robust proteases for the biorefinery industry. By targeting 340,000 clones from two libraries of pooled isolates of mesophilic and thermophilic marine bacteria and two libraries of microbial communities inhabiting marine environments, we identified proteases in four of eleven selected clones that showed activity against all substrates herein tested after prolonged incubation at 55 °C. Following sequencing, in silico analysis and recombinant expression in Escherichia coli, one functional protease, 58% identical at sequence level to previously reported homologs, was found to readily hydrolyze highly insoluble zein at temperatures up to 50 °C and pH 9–11. It is derived from a bacterial group whose ability to degrade zein was unknown. This study reports a two-step screen resulting in identification of a new marine metagenome-derived protease with zein-hydrolytic properties at common biomass processing temperatures that could be useful for the modern biorefinery industry.

Key points

• A two-step multi-substrate strategy for discovery of robust proteases.

• Feasible approach for shortening enzyme optimization to industrial demands.

• A new temperature-tolerant protease efficiently hydrolyzes insoluble zein.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11235-9.

Plant Growth Promotion Function of Bacillus sp. Strains Isolated from Salt-Pan Rhizosphere and Their Biocontrol Potential against Macrophomina phaseolina

In recent decades, intensive crop management has involved excessive use of pesticides or fertilizers, compromising environmental integrity and public health. Accordingly, there has been worldwide pressure to find an eco-friendly and safe strategy to ensure agricultural productivity. Among alternative approaches, Plant Growth-Promoting (PGP) rhizobacteria are receiving increasing attention as suitable biocontrol agents against agricultural pests. In the present study, 22 spore-forming bacteria were selected among a salt-pan rhizobacteria collection for their PGP traits and their antagonistic activity against the plant pathogen fungus Macrophomina phaseolina. Based on the higher antifungal activity, strain RHFS10, identified as Bacillus vallismortis, was further examined and cell-free supernatant assays, column purification, and tandem mass spectrometry were employed to purify and preliminarily identify the antifungal metabolites. Interestingly, the minimum inhibitory concentration assessed for the fractions active against M. phaseolina was 10 times lower and more stable than the one estimated for the commercial fungicide pentachloronitrobenzene. These results suggest the use of B. vallismortis strain RHFS10 as a potential plant growth-promoting rhizobacteria as an alternative to chemical pesticides to efficiently control the phytopathogenic fungus M. phaseolina.

Intrinsic Parameters and Bacterial Growth Prediction in a Brazilian Minimally Ripened Cheese (Coalho) during Refrigerated Storage

This study evaluated the microbiological and physicochemical characteristics in different commercial brands of a Brazilian minimally ripened (coalho) cheese during 60 days of storage under refrigeration. Combinations of maximum and minimum values of water activity and pH determined in cheese samples at refrigeration temperature (7°C) were used in a bacterial growth prediction analysis. Maximum growth rate (Grmax) was estimated for different pathogenic and/or spoilage bacteria using the ComBase Predictor. Results of microbiological characterization analyses showed persistent high counts for all monitored microbial groups ( Lactobacillus spp., Lactococcus spp., Enterococcus spp., Staphylococcus spp., Enterobacteriaceae, proteolytic and lipolytic microorganisms, and fungi) in cheese samples; no dominant microbial group was observed over time. Values of pH (6.03 ± 0.16 to 7.28 ± 0.55), acidity (0.15% ± 0.09% to 0.66% ± 0.26%), sodium chloride (1.05% ± 0.19% to 1.97% ± 0.75%), and water activity (0.948 ± 0.020 to 0.974 ± 0.012) did not vary in cheese samples during storage. Estimated Grmax values for the tested bacteria were in the range of 0.004 to 0.044 log CFU/h. Highest Grmax values (0.005 to 0.044 log CFU/h) were predicted for the psychrotrophic Aeromonas hydrophila, Listeria monocytogenes, Pseudomonas spp., and Yersinia enterocolitica. Grmax values predicted for Escherichia coli, Salmonella spp., and Staphylococcus aureus were in the range of 0.004 to 0.016 log CFU/h. These results indicate unsatisfactory microbiological characteristics of commercially available coalho cheese. Physicochemical characteristics of commercial coalho cheese stored under refrigeration allow bacterial growth to occur, indicating higher risk for fast growth of contaminant bacteria in this product.

Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose

Streptococcus thermophilus is a species widely used in the dairy industry for its capability to rapidly ferment lactose and lower the pH. The capability to use galactose produced from lactose hydrolysis is strain dependent and most of commercial S. thermophilus strains are galactose-negative (Gal⁻), although galactose-positive (Gal⁺) would be more technologically advantageous because this feature could provide additional metabolic products and prevent galactose accumulation in foods. In this study, a next generation sequencing transcriptome approach was used to compare for the first time a Gal⁺ and a Gal⁻ strain to characterize their whole metabolism and shed light on their different properties, metabolic performance and gene regulation. Transcriptome analysis revealed that all genes of the gal operon were expressed very differently in Gal⁺ and in the Gal⁻ strains. The expression of several genes involved in mixed acid fermentation, PTS sugars transporter and stress response were found enhanced in Gal⁺. Conversely, genes related to amino acids, proteins metabolism and CRISPR associated proteins were under-expressed. In addition, the strains showed a diverse series of predicted genes controlled by the transcriptional factor catabolite control protein A (CcpA). Overall, transcriptomic analysis suggests that the Gal⁺ strain underwent a metabolic remodeling to cope with the changed environmental conditions.

Current functional metagenomic approaches only expand the existing protease sequence space, but does not presently add any novelty to it

Proteases are a fundamental function in many organisms and thus many ecosystems and yet they are rarely obtained in functional metagenomic screens. Here, we have isolated an active protease gene (M1-2; 613 amino acids) which resided in a 38.4 kb fosmid clone that showed a classical protease-positive phenotype. It was classified as a zinc-dependent metalloprotease, with the closest annotated sequence as a neutral protease from Collimonas fungivorans (62 % similarity and 72 % homology). Further characterisation showed that its optimum temperature and pH were 42 °C and 8.0, respectively. Activity was inhibited by EDTA, but inhibition started to be reversed by excess Zn(2+). A putative signal peptide was identified bioinformatically and this may be why this protease was successfully isolated using a functional metagenomic screen. Bioinformatic analysis shows that this does not represent a novel protease, but simply expands the current sequence space of known proteases.