Microbial Evolution Research Articles

Novel integrative elements and genomic plasticity in ocean ecosystems

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.

Gut immune responses and evolution of the gut microbiome-a hypothesis.

The gut microbiome is an assemblage of microbes that have profound effects on their hosts. The composition of the microbiome is affected by bottom-up, among-taxa interactions and by top-down, host effects, which includes the host immune response. While the high-level composition of the microbiome is generally stable over time, component strains and genotypes will constantly be evolving, with both bottom-up and top-down effects acting as selection pressures, driving microbial evolution. Secretory IgA is a major feature of the gut's adaptive immune response, and a substantial proportion of gut bacteria are coated with IgA, though the effect of this on bacteria is unclear. Here we hypothesize that IgA binding to gut bacteria is a selection pressure that will drive the evolution of IgA-bound bacteria, so that they will have a different evolutionary trajectory than those bacteria not bound by IgA. We know very little about the microbiome of wild animals and even less about their gut immune responses, but it must be a priority to investigate this hypothesis to understand if and how host immune responses contribute to microbiome evolution.

Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals

BackgroundAnimals form complex symbiotic associations with their gut microbes, whose evolution is determined by an intricate network of host and environmental factors. In many insects, such as Drosophila melanogaster, the microbiome is flexible, environmentally determined, and less diverse than in mammals. In contrast, mammals maintain complex multispecies consortia that are able to colonize and persist in the gastrointestinal tract. Understanding the evolutionary and ecological dynamics of gut microbes in different hosts is challenging. This requires disentangling the ecological factors of selection, determining the timescales over which evolution occurs, and elucidating the architecture of such evolutionary patterns.ResultsWe employ experimental evolution to track the pace of the evolution of a common gut commensal, Lactiplantibacillus plantarum, within invertebrate (Drosophila melanogaster) and vertebrate (Mus musculus) hosts and their respective diets. We show that in Drosophila, the nutritional environment dictates microbial evolution, while the host benefits L. plantarum growth only over short ecological timescales. By contrast, in a mammalian animal model, L. plantarum evolution results to be divergent between the host intestine and its diet, both phenotypically (i.e., host-evolved populations show higher adaptation to the host intestinal environment) and genomically. Here, both the emergence of hypermutators and the high persistence of mutated genes within the host’s environment strongly differed from the low variation observed in the host’s nutritional environment alone.ConclusionsOur results demonstrate that L. plantarum evolution diverges between insects and mammals. While the symbiosis between Drosophila and L. plantarum is mainly determined by the host diet, in mammals, the host and its intrinsic factors play a critical role in selection and influence both the phenotypic and genomic evolution of its gut microbes, as well as the outcome of their symbiosis.

Microbial micro-tube culture system: A miniature bioreactor for controllable bubble-free oxygen supply based on high gas-permeability Teflon tube

Here a novel micro-tube bioreactor (MTB) was reported based on the high gas-permeability Teflon tube, realizing controllable and bubble-free oxygen supply with low shear stress during microbial cultivation. It was validated by cultivating six microbial strains in MTB and conventional shake flasks, where improved growth performance was achieved in MTB with regards to the incipient growth rate and terminal biomass accumulation. Typical fed-batch cultivation of Bacillus subtilis was conducted in MTB to enable high-density microbial cultivation, which has tripled in biomass accumulation from batch mode. Adaptive evolution against oxygen for Lactobacillus plantarum was performed through an 8-day cultivation process under escalating oxygen partial pressure from 5 % to 20 % in MTB, and remarkably improved growth performance was obtained in aerobic environment in comparison with the parent strain (with biomass accumulation increased by 130–150 %). MTB is demonstrated to be a promising platform for controllable bubble-free oxygen supply with automated and easy operation for microbial cultivation and adaptive evolution.

Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria.

Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.

Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station

BackgroundMonitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS.ResultsHere, we report how ISS-associated A. pittii (n = 20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n = 291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host-associated ISS metagenomes, we observed that viable A. pittii is increasing in relative abundance and therefore potentially exhibiting succession, being identified in >2X more metagenomic samples in back-to-back missions. ISS strains additionally contain functions that enable them to survive in harsh environments, including the transcriptional regulator LexA. Via a genome-wide association study, we identified a high level of mutational burden in methionine sulfoxide reductase genes relative to the most closely related Earth strains.ConclusionsOverall, these results indicated a step forward in understanding how microorganisms might evolve and alter their antibiotic resistance phenotype in extreme, resource-limited, human-built environments.7sQ1goT5P8_QSQ1VpYZNydVideo

Microbial Community and Their Potential Functions after Natural Vegetation Restoration in Gullies of Farmland in Mollisols of Northeast China

Although huge numbers of gullies have been widely formed and have severely decreased the quality of farmlands in mollisols, it is still unclear how the microbial community distributes after natural vegetation restoration (NVR), which highly relates to the ecological functions in the farmland. In this study, both the microbial community and their potential ecological functions after NVR were reviewed, together with the environmental factors relating to microbial evolution which were detected in two gullies of mollisols situated on farmland in Northeast China. The main results showed that NVR improved the microbial diversity and complexity of the co-occurrence network in gullies, and promoted bacterial community composition to be similar between the gully and deposition area. Moreover, the soil organic matter (SOM) regulated the microbial diversity by balancing soil available phosphorus (AP), soil moisture (SM), and pH, thus stimulating the key bacterial biomarkers of gullies (Rhizobiales, Microtrichales, TRA3-20) and regulating the bacterial composition, as well as indirectly enriching the function of bacteria to perform denitrification, C fixation, and phosphorus transport in gullies. In addition, abundant Dicotyledons in gullies mainly regulate the fungal community composition, and increased fungal richness in 0–20 cm soil depth, but decreased bacteria richness in 0–20 cm soil depth. Our findings revealed the repair mechanism of NVR on soil bacterial and fungal communities, especially on bacterial functionality, which should be given further attention in nutrient cycling across eroding mollisols in gullies.

Phenotypic plasticity as a facilitator of microbial evolution.

Tossed about by the tides of history, the inheritance of acquired characteristics has found a safe harbor at last in the rapidly expanding field of epigenetics. The slow pace of genetic variation and high opportunity cost associated with maintaining a diverse genetic pool are well-matched by the flexibility of epigenetic traits, which can enable low-cost exploration of phenotypic space and reactive tuning to environmental pressures. Aiding in the generation of a phenotypically plastic population, epigenetic mechanisms often provide a hotbed of innovation for countering environmental pressures, while the potential for genetic fixation can lead to strong epigenetic-genetic evolutionary synergy. At the level of cells and cellular populations, we begin this review by exploring the breadth of mechanisms for the storage and intergenerational transmission of epigenetic information, followed by a brief review of common and exotic epigenetically regulated phenotypes. We conclude by offering an in-depth coverage of recent papers centered around two critical issues: the evolvability of epigenetic traits through Baldwinian adaptive phenotypic plasticity and the potential for synergy between epigenetic and genetic evolution.

The Use of a Multimodal Case Study To Illustrate Microbial Genetics, Metabolism, and Evolution: The Emergence of VRSA-1.

Antibiotic Resistance (ABR) is a global concern and while many students are aware of this issue, many of them are unclear on the mechanisms by which ABR may emerge. The mechanism of horizontal gene transfer is something many students are not familiar with. In this curriculum contribution we present 2 versions of an 'interrupted case study' that is designed as an introduction to horizontal gene transfer for early major students and as a review case for advanced major students in biology and life sciences. The case is based on an authentic patient who developed infections with both methicillin resistant Staphylococcus aureus and vancomycin resistant S. aureus. The interrupted case study is appropriate for small and large groups and engages students while content is introduced in a highly structured way. This type of case study can be done by novice and seasoned instructors and lead to considerable learning gains in both introductory and intermediate microbiology courses.

Towards quantifying microbial dispersal in the environment.

Towards quantifying microbial dispersal in the environment.

Reconstructing horizontal gene flow network to understand prokaryotic evolution.

Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches. Here, we exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. Our network is unique in its ability to detect the transfer of native genes of a genome to genomes from other taxa, thus establishing donor and recipient organisms (taxa), rather than through a post hoc analysis as is the practice with several other approaches. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.

Predicting selection for antimicrobial resistance in UK wastewater and aquatic environments: Ciprofloxacin poses a significant risk.

Antimicrobial resistance (AMR) is a threat to human and animal health, with the environment increasingly recognised as playing an important role in AMR evolution, dissemination, and transmission. Antibiotics can select for AMR at very low concentrations, similar to those in the environment, yet their release into the environment, e.g., from wastewater treatment plants, is not currently regulated. Understanding the selection risk antibiotics pose in wastewater and receiving waters is key to understanding if environmental regulation of antibiotics is required. We investigated the risk of selection occurring in UK wastewater and receiving waters by determining where measured environmental concentration data (n=8187) for four antibiotics (ciprofloxacin, azithromycin, clarithromycin, and erythromycin) collected in England and Wales 2015-2018 (sites n=67) exceeded selective concentration thresholds derived from complex microbial community evolution experiments undertaken previously. We show that selection for AMR by ciprofloxacin is likely to have occurred routinely in England and Wales wastewater during the 2015-2018 period, with some seasonal and regional trends. Wastewater treatment reduces the selection risk posed by ciprofloxacin significantly, but not completely, and predicted risk in surface waters remains high in several cases. Conversely, the potential risks posed by the macrolides (azithromycin, clarithromycin, and erythromycin) were lower than those posed by ciprofloxacin. Our data demonstrate further action is needed to prevent selection for AMR in wastewater, with environmental quality standards for some antibiotics required in the future, and that selection risk is not solely a concern in low/middle income countries.

Long-term performance, microbial evolution and spatial microstructural characteristics of anammox granules in an upflow blanket filter (UBF) treating high-strength nitrogen wastewater

Granule formation, microstructure and microbial spatial distribution are crucial to granule stability and nitrogen removal. Here, an upflow blanket filter (UBF) reactor with porous fixed cylinder carriers was fabricated and operated for 234 days to investigate overall performance and the formation mechanism of anammox granules. Results showed that the UBF performed the highest nitrogen removal efficiency of 93.19 ± 3.39% under nitrogen loading rate of 3.6 kg-N/m3/d and HRT of 2 h. The tryptophan-like proteins as the key component in EPS were vital for granules formation. Further 16 s rRNA analysis indicated that SBR1031 with a relative abundance of 40.5% played an important role in cell aggregation. Thus, anammox granules were developed successfully with a two-layered spatial structure where outer-layer was ammonia oxidizing bacteria and inner-core was anaerobic ammonia oxidizing bacteria. Together, introduction of porous fixed cylinder carriers is a valid method to avoid biomass loss and floatation.

Simultaneous nitrification and denitrification in a PCL-supported constructed wetland with limited aeration.

Considerable advances have been made in the substrate design and operation strategies of constructed wetlands to facilitate nitrogen elimination. However, few studies examined the complicated interaction between solid organic substrates and limited aeration on nitrogen removal. A vertical flow constructed wetlands in gradient distribution of inorganic and solid organic substrates (polycaprolactone/PCL) (P-VFCW) and a controlled vertical flow constructed wetland without PCL (C-VFCW) were developed for the tertiary treatment of municipal tailwater. Results indicated that ammonia was nearly converted to nitrate, while the total nitrogen removal efficiencies (TNREs) in C-VFCW were negligible. In P-VFCW, however, optimal TNREs approached 95% with an aeration rate of 0.06mL·min-1 and hydraulic retention time (HRT) of 24h, and simultaneous nitrification and denitrification process (SND) in aerobic conditions was confirmed. As for the spatial microbial community structure evolution, Comamonas, which is associated with heterotrophic nitrification and anoxic/aerobic denitrification, was enriched along the vertical profiles of P-VFCW. Autotrophic nitrifier (Nitrospira), aerobic denitrifier (Bradyrhizobium and Azospira), and anoxic denitrifier (Ignavibacterium and Methyloversatilis) were dominated in different depths of P-VFCW, respectively. Besides, Canna indica biomass in P-VFCW was significantly larger than that in C-VFCW, which was attributed to the plant adaption response to diverse nitrogen. The P-VFCW in gradient distribution of inorganic and solid carbon sources under limited aeration is a promising technology for advanced nitrogen removal.

Genomic evolution of SARS-CoV-2 in Reunion Island.

Island communities are interesting study sites for microbial evolution during epidemics, as their insular nature reduces the complexity of the population's connectivity. This was particularly true on Reunion Island during the first half of 2021, when international travel was restricted in order to mitigate the risk for SARS-CoV-2 introductions. Concurrently, the SARS-CoV-2 Beta variant became dominant and started to circulate at high levels for several months before being completely replaced by the Delta variant as of October 2021. Here, we explore some of the particularities of SARS-CoV-2 genomic evolution within the insular context of Reunion Island. We show that island isolation allowed the amplification and expansion of unique genetic lineages that remained uncommon across the globe. Islands are therefore potential hotspots for the emergence of new genetic variants, meaning that they will play a key role in the continued evolution and propagation of COVID-19 as the pandemic persists.

A history of the MetaSUB consortium: Tracking urban microbes around the globe

SummaryThe MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.

Phenotypic selection during laboratory evolution of yeast populations leads to a genome-wide sustainable chromatin compaction shift.

In a previous study, we have shown how microbial evolution has resulted in a persistent reduction in expression after repeatedly selecting for the lowest PGAL1-YFP-expressing cells. Applying the ATAC-seq assay on samples collected from this 28-day evolution experiment, here we show how genome-wide chromatin compaction changes during evolution under selection pressure. We found that the chromatin compaction was altered not only on GAL network genes directly impacted by the selection pressure, showing an example of selection-induced non-genetic memory, but also at the whole-genome level. The GAL network genes experienced chromatin compaction accompanying the reduction in PGAL1-YFP reporter expression. Strikingly, the fraction of global genes with differentially compacted chromatin states accounted for about a quarter of the total genome. Moreover, some of the ATAC-seq peaks followed well-defined temporal dynamics. Comparing peak intensity changes on consecutive days, we found most of the differential compaction to occur between days 0 and 3 when the selection pressure was first applied, and between days 7 and 10 when the pressure was lifted. Among the gene sets enriched for the differential compaction events, some had increased chromatin availability once selection pressure was applied and decreased availability after the pressure was lifted (or vice versa). These results intriguingly show that, despite the lack of targeted selection, transcriptional availability of a large fraction of the genome changes in a very diverse manner during evolution, and these changes can occur in a relatively short number of generations.

The effect of fishing season and storage conditions on the quality of European plaice (Pleuronectes platessa)

The combined effect of fishing season (September/April) and storage conditions on the quality of European plaice (Pleuronectes platessa) was investigated. Investigated storage conditions were; fillets packaged in vacuum or a modified atmosphere (MA; 70% CO2, 20% N2, 10% O2) and stored at 4 °C. As a control, whole fish on ice (0 °C) was used, representing the commercial standard. Plaice showed in general lower quality in April than September, demonstrated by a faster microbial evolution, higher content of biogenic amines, and higher rate of ATP degradation representing by K- and H-values. MA-fillets and whole fish on ice showed lower K- and H-values and biogenic amines content than fillets packaged in vacuum. VP-fillets had the lowest microbial quality as demonstrated by the shortest lag-phase of psychrotrophic aerobic plate count and aerobic bacteria, and the highest maximum specific growth rate of H2S-producing bacteria. MA packaging significantly reduced microbial growth; however, MA-fillets showed the lowest water content and the highest drip loss and water holding capacity. No differences between groups were observed in colour intensity or hue angle at the storage end. Despite the significant seasonal variations, MA packaging stands out as the best solution to maintain the freshness of convenient retail plaice products.

Experimental test of the contributions of initial variation and new mutations to adaptive evolution in a novel environment

Experimental evolution is an approach that allows researchers to study organisms as they evolve in controlled environments. Despite the growing popularity of this approach, there are conceptual gaps among projects that use different experimental designs. One such gap concerns the contributions to adaptation of genetic variation present at the start of an experiment and that of new mutations that arise during an experiment. The primary source of genetic variation has historically depended largely on the study organisms. In the long-term evolution experiment (LTEE) usingEscherichia coli, for example, each population started from a single haploid cell, and therefore, adaptation depended entirely on new mutations. Most other microbial evolution experiments have followed the same strategy. By contrast, evolution experiments using multicellular, sexually reproducing organisms typically start with preexisting variation that fuels the response to selection. New mutations may also come into play in later generations of these experiments, but it is generally difficult to quantify their contribution in these studies. Here, we performed an experiment usingE. colito compare the contributions of initial genetic variation and new mutations to adaptation in a new environment. Our experiment had four treatments that varied in their starting diversity, with 18 populations in each treatment. One treatment depended entirely on new mutations, while the other three began with mixtures of clones, whole-population samples, or mixtures of whole-population samples from the LTEE. We tracked a genetic marker associated with different founders in two treatments. These data revealed significant variation in fitness among the founders, and that variation impacted evolution in the early generations of our experiment. However, there were no differences in fitness among the treatments after 500 or 2,000 generations in the new environment, despite the variation in fitness among the founders. These results indicate that new mutations quickly dominated, and eventually they contributed more to adaptation than did the initial variation. Our study thus shows that preexisting genetic variation can have a strong impact on early evolution in a new environment, but new beneficial mutations may contribute more to later evolution and can even drive some initially beneficial variants to extinction.

Two-Phase improves Bio-hydrogen and Bio-methane production of anaerobic membrane bioreactor from waste activated sludge with digestate recirculation

The conventional recirculated two-phase anaerobic digestion (R-TPAD) equipped with two continuous stirred tank reactors (CSTR) usually shows poor water quality, insufficient bioconversion degree and low methane productivity. In this study, a new R-TPAD with CSTR as acidogenic phase and anaerobic membrane reactor (AnMBR) as methanogenic phase was constructed to digest waste activated sludge (WAS) for renewable energy recovery (H2 and CH4). The effects of recirculation ratio (R) on start-up time, long-term performance, membrane fouling behaviors, microbial community evolution, and energy recovery efficiencies were investigated systematically. Result showed that the R-TPAD possessed high H2 (6.1 mL/g-COD) and CH4 (67.9 mL/g-COD) yields with the corresponding COD removal of up to 96.1% at R0.2. During the whole process, the transmembrane pressure was lower than −3.3 kPa with negligible membrane fouling observed. The 16S rRNA gene analysis revealed that the synergistic role of membrane separation and recirculation system promoted the proliferation of fatty acids-producing and organics-degrading bacteria (i.e. Coprothermobacteraeota, Bacteroidetes, etc.) in acidogenic phase and CH4-producing methanogens (i.e. Methanobacterium, Methanosaeta, etc.) in methanogenic phase, thus accelerating the biodegradation of WAS. This positive stimulation sustained the high diversity and the dynamic balance of key microorganisms in the R-TPAD process. Energy balance analysis further indicated that the R-TPAD with R0.2 could increase net energy output by 77.9% compared to the control TPAD without recirculation. This work provides a fundamental data base for the scientific management of WAS and push forward the real-world application of R-TPAD technology in the real-world scenarios.