High antagonistic activity and antibiotic resistance of flavobacteria of polar microbial freshwater mats on King George Island in maritime Antarctica

This is the first study to demonstrate a relationship between antagonistic interactions with antibiotic resistance within flavobacterial strains, a component of polar-region microbial mats. These strains were derived from ephemeral freshwater reservoirs, i.e. ponds and streams of the periglacial zone of Ecology Glacier (King George Island, maritime Antarctica). The study demonstrated the strains' surprisingly high phylogenetic diversity, with 20 species among 50 isolates. Flavobacteria were characterised by different patterns of antagonism and sensitivity to antimicrobials. 29 strains produced substances inhibiting the growth of other isolates, with 21 strains being sensitive to such compounds; 34 strains were multidrug-resistant (MDR). The antibiotic resistance index (ARI) demonstrated a significantly higher proportion of MDR strains and ARI ≥ 0.2 in stream mats (87%) as compared to the strains derived from pond mats (55%). A strong correlation was observed between the strains' antagonistic potential and antibiotic resistance. An important role in these phenomena is accomplished by the "super bacteria" strains that effectively accumulate numerous traits associated with antagonistic potential and can be involved in the potential transfer of these traits. The results of the study demonstrate that there are individual patterns of antagonistic interactions and antibiotic resistance among the biotic components of mats.

Psychrotrophic Antarctic marine bacteria as potential reservoirs for novel antimicrobial genes

Antarctica is a very cold, isolated continent surrounded by frozen seas, yet these extreme environmental conditions have not restricted life and diversity in the sea. The marine environment is seasonally highly productive and harbours diverse and abundant communities of organisms, with many endemic species occurring nowhere else in the world. Such communities and their associated microbiomes are increasingly recognized as an unexplored source of novel antimicrobial products. Hence, the major aim of this study was to examine the antimicrobial potential of bacteria cultured from eight Antarctic marine invertebrate species, while gathering data on Antarctic microbial thermal and salinity tolerances. All cultured bacterial species (n = 34) were related to known psychrotrophs, with thermal tolerances that far exceeded those of their invertebrate hosts. Of note, two strains of Psychrobacter and Pseudomonas produced antagonistic activity towards epidemic methicillin-resistant Staphylococcus aureus, Micrococcus luteus, and Candida albicans in preliminary simultaneous antagonism screens. Draft whole genome sequence analysis revealed the presence of 13 biosynthetic gene clusters; including those with potential to produce betalactones, post-translationally modified peptide products, and arylpropynes. These results emphasize the need for more extensive and systematic surveys to identify novel biomolecules from Antarctic marine bacteria that may be exploited for societal gain.

Analytical strategy to assess the microbial degradation of poly(butylene-adipate-co-terephthalate)/poly(lactic acid) films

Plastic is widely used in agricultural applications, but its waste has an adverse environmental impact and a long-term detrimental effect. The development of biodegradable plastics for agricultural use is increasing to mitigate plastic waste. The most commonly used biodegradable plastic is poly(butylene adipate co-terephthalate)/poly(lactic acid) (PBAT/PLA) polymer. In this study, an analytical procedure based on dispersive liquid-liquid microextraction (DLLME) followed by gas chromatography-mass spectrometry (GC-MS) in combination with chemometrics has been optimized to assess the degradation level of PBAT/PLA films by monitoring their characteristic degradation products. Carboxylic acids (benzoic, phthalic, adipic, heptanoic, and octadecanoic acids) and 1,4-butanediol have been found to be potential markers of PBAT/PLA degradation. The DLLME-GC-MS analytical approach has been applied for the first time to assess the degradation efficiency of several microorganisms used as degradation accelerators of PBAT/PLA based on the assigned potential markers. This analytical strategy has shown higher sensitivity and precision than standard techniques, such as elemental analysis, allowing us to detect low degradation levels.

Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil

Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.

Nested structure of intraspecific competition network in Carnobacterium maltaromaticum

While competition targeting food-borne pathogens is being widely documented, few studies have focused on competition among non-pathogenic food bacteria. Carnobacterium maltaromaticum is a genetically diverse lactic acid bacterium known for comprising several bacteriocinogenic strains with bioprotective potentialities against the food-borne pathogen Listeria monocytogenes. The aim of our study is to examine the network properties of competition among a collection of 73 strains of C. maltaromaticum and to characterize their individual interaction potential. The performed high-throughput competition assays, investigating 5 329 pairwise interactions, showed that intraspecific competition was major in C. maltaromaticum with approximately 56% of the sender strains antagonizing at least one receiver strain. A high diversity of inhibitory and sensitivity spectra was identified along with a majority of narrow inhibitory as well as sensitivity spectra. Through network analysis approach, we determined the highly nested architecture of C. maltaromaticum competition network, thus showing that competition in this species is determined by both the spectrum width of the inhibitory activity of sender strains and the spectrum width of the sensitivity of receiver strains. This study provides knowledge of the competition network in C. maltaromaticum that could be used in rational assembly of compatible microbial strains for the design of mixed starter cultures.

Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils

Soil microbes live within highly complex communities, where community composition, function, and evolution are the product of diverse interactions among community members. Analysis of the complex networks of interactions within communities has the potential to shed light on community stability, functioning, and evolution. However, we have little understanding of the variation in interaction networks among coevolved soil populations. We evaluated networks of antibiotic inhibitory interactions among sympatric Streptomyces communities from prairie soil. Inhibition networks differed significantly in key network characteristics from expectations under null models, largely reflecting variation among Streptomyces in the number of sympatric populations that they inhibited. Moreover, networks of inhibitory interactions within Streptomyces communities differed significantly from each other, suggesting unique network structures among soil communities from different locations. Analyses of tri-partite interactions (triads) showed that some triads were significantly over- or under- represented, and that communities differed in ‘preferred’ triads. These results suggest that local processes generate distinct structures among sympatric Streptomyces inhibition networks in soil. Understanding the properties of microbial interaction networks that generate competitive and functional capacities of soil communities will shed light on the ecological and coevolutionary history of sympatric populations, and provide a foundation for more effective management of inhibitory capacities of soil microbial communities.

Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect

Background

Growing concern about the emergence of antibiotic resistance is compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of genome sequences has enabled the development of computational mining as an important tool in the discovery of natural products with antibiotic effect.

Results

NRPPUR (Non-Ribosomal Peptide and Polyketide Urmite) is a new bioinformatic tool that was created to detect polyketides and non-ribosomal peptide gene clusters (PKS and NRPS) in bacterial genomes using the rpsBlast program. The NRPPUR database was constructed locally by assembling all 3505 available sequences of NRPS-PKS that have been identified by in silico approaches to date, with 164 Biosynthetic Gene Clusters (BGCs) derived from the published literature that have demonstrated antimicrobial activity in vitro. The in silico analysis of 49 intestinal human bacterial genomes using the NRPPUR made it possible to identify 91 BGCs including 89 clusters that had never previously been described. On average, intestinal human bacterial genomes devote nearly 0.8% (±1.4% s.d.) of their genome to NRPS/PKS biosynthesis, with Bacillus vallismortis, Streptomyces massiliensis and Bacillus subtilis genomes apportioning 8.4, 3.6 and 3.15% of their genomes, respectively. When using the cross-streak method, S. massiliensis displayed antibacterial activity against many Gram-positive and negative bacteria including methicillin-resistant Staphylococcus aureus (MRSA).

Conclusions

NRPPUR has proven to be a very useful tool for the primary in silico selection of species with potential antimicrobial activity and human microbiota could be the future source of new antimicrobial discoveries. Further exploration of this and other ecological niches, coupled with high-throughput antibacterial activity screening should be envisaged.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2479-5) contains supplementary material, which is available to authorized users.

Three-species competition with non-deterministic outcomes

Theoretical and experimental research studies have shown that ecosystems governed by non-transitive competition networks tend to maintain high levels of biodiversity. The theoretical body of work, however, has mainly focused on competition networks in which the outcomes of competition events are predetermined and hence deterministic, and where all species are identical up to their competitive relationships, an assumption that may limit the applicability of theoretical results to real-life situations. In this paper, we aim to probe the robustness of the link between biodiversity and non-transitive competition by introducing a three-dimensional winning probability parameter space, making the outcomes of competition events in a three-species in silico ecosystem uncertain. While two degenerate points in this parameter space have been the subject of previous studies, we investigate the remaining settings, which equip the species with distinct competitive abilities. We find that the impact of this modification depends on the spatial dimension of the system. When the system is well mixed, it collapses to monoculture, as is also the case in the non-transitive deterministic setting. In one dimension, chaotic patterns emerge, which tend to maintain biodiversity, and a power law relates the time that species manage to coexist to the degree of uncertainty regarding competition event outcomes. In two dimensions, the formation of spiral wave patterns ensures that biodiversity is maintained for moderate degrees of uncertainty, while considerable deviations from the non-transitive deterministic setting have strong negative effects on species coexistence. It can hence be concluded that non-transitive competition can still produce coexistence when the assumption of deterministic competition is abandoned. When the system collapses to monoculture, one observes a "survival of the strongest" law, as the species that has the highest probability of defeating its competitors has the best odds to become the sole survivor.

Complex carbohydrates reduce the frequency of antagonistic interactions among bacteria degrading cellulose and xylan

Bacterial competition for resources is common in nature but positive interactions among bacteria are also evident. We speculate that the structural complexity of substrate might play a role in mediating bacterial interactions. We tested the hypothesis that the frequency of antagonistic interactions among lignocellulolytic bacteria is reduced when complex polysaccharide is the main carbon source compared to when a simple sugar such as glucose is available. Results using all possible pairwise interactions among 35 bacteria isolated from salt marsh detritus showed that the frequency of antagonistic interactions was significantly lower on carboxymethyl cellulose (CMC)-xylan medium (7.8%) than on glucose medium (15.5%). The two interaction networks were also different in their structures. Although 75 antagonistic interactions occurred on both media, there were 115 that occurred only on glucose and 20 only on CMC-xylan, indicating that some antagonistic interactions were substrate specific. We also found that the frequency of antagonism differed among phylogenetic groups. Gammaproteobacteria and Bacillus sp. were the most antagonistic and they tended to antagonize Bacteroidetes and Actinobacteria, the most susceptible groups. Results from the study suggest that substrate complexity affects how bacteria interact and that bacterial interactions in a community are dynamic as nutrient conditions change.

Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal Lake in the Indian trans-Himalayas

The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852^T and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852^T and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596^T (97.8% and 97.7%) and less than 95.9% similarity to other species of the genus Paenibacillus. DNA-DNA relatedness among strains IHBB 9852^T and IHBB 9951 was 90.2%, and with P. lactis DSM 15596^T, was 52.7% and 52.4%, respectively. The novel strains contain anteiso-C_15:0, iso-C_15:0, C_16:0 and iso-C_16:0 as major fatty acids, and phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol were predominant polar lipids. The DNA G+C content for IHBB 9852T and IHBB 9951 was 52.1 and 52.2mol%. Based on the results of phenotypic and genomic characterisations, we concluded that strains IHBB 9852^T and IHBB 9951 belong to a novel Paenibacillus species, for which the name Paenibacillus ihbetae sp. nov. is proposed. The type strain is IHBB 9852^T (=MTCC 12459^T=MCC 2795^T=JCM 31131^T=KACC 19072^T; DPD TaxonNumber TA00046) and IHBB 9951 (=MTCC 12458=MCC 2794=JCM 31132=KACC 19073) is a reference strain.

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion.

Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils

Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils.

Microbial competition in polar soils: a review of an understudied but potentially important control on productivity

Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants.