Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases

Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.

Comparative Genomics Analysis of Habitat Adaptation by Lactobacillus kefiranofaciens

Lactobacillus kefiranofaciens is often found in fermented dairy products. Many strains of this species have probiotic properties, contributing to the regulation of immune metabolism and intestinal flora. This species was added to the list of lactic acid bacteria that can be added to food in China, in 2020. However, research on the genomics of this species is scarce. In this study we undertook whole genome sequencing analysis of 82 strains of L. kefiranofaciens from different habitats, of which 9 strains were downloaded from the NCBI RefSeq (National Center for Biotechnology Information RefSeq). The mean genome size of the 82 strains was 2.05 ± 0.25 Mbp, and the mean DNA G + C content was 37.47 ± 0.42%. The phylogenetic evolutionary tree for the core genes showed that all strains belonged to five clades with clear aggregation in relation to the isolation habitat; this indicated that the genetic evolution of L. kefiranofaciens was correlated to the isolation habitat. Analysis of the annotation results identified differences in the functional genes, carbohydrate active enzymes (CAZy) and bacteriocins amongst different isolated strains, which were related to the environment. Isolates from kefir grains had more enzymes for cellulose metabolism and a better ability to use vegetative substrates for fermentation, which could be used in feed production. Isolates from kefir grains also had fewer kinds of bacteriocin than isolates from sour milk and koumiss; helveticin J and lanthipeptide class I were not found in the isolates from kefir grains. The genomic characteristics and evolutionary process of L. kefiranofaciens were analyzed by comparative genomics and this paper explored the differences in the functional genes amongst the strains, aiming to provide a theoretical basis for the research and development of L. kefiranofaciens.

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses

SignificanceIn marine ecosystems, transmission of microbial symbionts between host generations occurs predominantly through the environment. Yet, it remains largely unknown how host genetics, symbiont competition, environmental conditions, and geography shape the composition of symbionts acquired by individual hosts. To address this question, we applied population genomic approaches to four species of deep-sea hydrothermal vent snails that live in association with chemosynthetic bacteria. Our analyses show that environment is more important to strain-level symbiont composition than host genetics and that symbiont strains show genetic variation indicative of adaptation to the distinct geochemical conditions at each vent site. This corroborates a long-standing hypothesis that hydrothermal vent invertebrates affiliate with locally adapted symbiont strains to cope with the variable conditions characterizing their habitats.

Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species. IMPORTANCE Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood. Here, we show that the population structure of a ubiquitous Streptomyces species complex matches its habitat distribution and can be defined by gene flow discontinuities. Using comparative genomics and physiological assays, we reveal that gains and losses of specific genomic traits play a significant role in the transition between free-living and host-associated lifestyles, driving speciation of the species. These results provide new insights into the evolutionary trajectory of Streptomyces and the notion of species.

Polyploidy Improves Photosynthesis Regulation within the Ranunculus auricomus Complex (Ranunculaceae)

Simple Summary

Genome duplication or multiplication, polyploidy, has contributed substantially to the evolutionary success of plants. Polyploidy is often connected to a higher resilience to environmental stress. We have chosen the goldilocks, the Ranunculus auricomus complex, to study effects of light stress. In this species complex, diploid (2x), tetraploid (4x), and hexaploid (6x) cytotypes occur in Central Europe in both shaded and sun-exposed habitats. In this study, we exposed them to different photoperiods in climate growth chambers to explore how the efficiency of photosynthesis varied between the various ploidies (2x, 4x, and 6x). We used fluorescence experiments exploring the proportion of light that is captured for photosynthesis and the resulting energy fluxes. In addition, quenching coefficients can be calculated that inform about the capability of a plant to deal with excess light. We found that the polyploids can quench excess light better, which concurs with their adaptation to open habitats and their predominantly asexual mode of reproduction that is probably favored by low stress levels in the reproductive tissues.

Abstract

Polyploidy has substantially contributed to successful plant evolution, and is often connected to a higher resilience to environmental stress. We test the hypothesis that polyploids tolerate light stress better than diploids. The Ranunculus auricomus complex comprises diploid (2x), tetraploid (4x), and hexaploid (6x) cytotypes, the former of which occur in shaded habitats and the latter more in open, sun-exposed habitats in Central Europe. In this study, we experimentally explored the effects of ploidy and photoperiod extension on the efficiency of photosystem II in the three cytotypes in climate growth chambers. Quantum yields and various coefficients that can be calculated from light curve, Kautsky curve, and fluorescent transient OJIP experiments provided support for the hypothesis that, in comparison to diploids, the improved regulation of excess light by more efficient photochemical and non-chemical quenching in polyploids might have facilitated the adaptation to unshaded habitats. We suggest how lower stress levels in reproductive tissues of polyploids might have favored asexual reproduction.

Biodiversity of Lactobacillus helveticus isolates from dairy and cereal fermentations reveals habitat-adapted biotypes

For the present study, we collected 22 Lactobacillus helveticus strains from different dairy (n = 10) and cereal (n  = 12) fermentations to investigate their biodiversity and to uncover habitat-specific traits. Biodiversity was assessed by comparison of genetic fingerprints, low-molecular-weight subproteomes, metabolic and enzymatic activities, growth characteristics and acidification kinetics in food matrices. A clear distinction between the dairy and cereal strains was observed in almost all examined features suggesting that the different habitats are domiciled by different L. helveticus biotypes that are adapted to the specific environmental conditions. Analysis of the low-molecular-weight subproteome divided the cereal isolates into two clusters, while the dairy isolates formed a separate homogeneous cluster. Differences regarding carbohydrate utilization were observed for lactose, galactose, sucrose and cellobiose as well as for plant-derived glucosides. Enzymatic differences were observed mainly for ß-galactosidase and ß-glucosidase activities. Further, growth temperature was optimal in the range from 33 to 37°C for the cereal strains, whereas the dairy strains showed optimal growth at 40°C. Taken together, adaptation of the various biotypes results in a growth benefit in the particular environment. Acidification and growth tests using either sterile skim milk or a wheat flour extract confirmed these results. Differentiation of these biotypes and their physiological characteristics enables knowledge-based starter culture development for cereal versus dairy products within one species.

Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment

In order to investigate the role of differential adaptation for the evolution of reproductive barriers, we conducted a multi-site transplant experiment with the dioecious sister species Silene dioica and S. latifolia and their hybrids. Crosses within species as well as reciprocal first-generation (F₁ ) and second-generation (F₂ ) interspecific hybrids were transplanted into six sites, three within each species' habitat. Survival and flowering were recorded over 4 yr. At all transplant sites, the local species outperformed the foreign species, reciprocal F₁ hybrids performed intermediately and F₂ hybrids underperformed in comparison to F₁ hybrids (hybrid breakdown). Females generally had slightly higher cumulative fitness than males in both within- and between-species crosses and we thus found little evidence for Haldane's rule acting on field performance. The strength of selection against F₁ and F₂ hybrids as well as hybrid breakdown increased with increasing strength of habitat adaptation (i.e. the relative fitness difference between the local and the foreign species) across sites. Our results suggest that differential habitat adaptation led to ecologically dependent post-zygotic reproductive barriers and drives divergence and speciation in this Silene system.

Fungal endophytes for sustainable crop production

This minireview highlights the importance of endophytic fungi for sustainable agriculture and horticulture production. Fungal endophytes play a key role in habitat adaptation of plants resulting in improved plant performance and plant protection against biotic and abiotic stresses. They encode a vast variety of novel secondary metabolites including volatile organic compounds. In addition to protecting plants against pathogens and pests, selected fungal endophytes have been used to remove animal toxicities associated with fungal endophytes in temperate grasses, to create corn and rice plants that are tolerant to a range of biotic and abiotic stresses, and for improved management of post-harvest control. We argue that practices used in plant breeding, seed treatments and agriculture, often caused by poor knowledge of the importance of fungal endophytes, are among the reasons for the loss of fungal endophyte diversity in domesticated plants and also accounts for the reduced effectiveness of some endophyte strains to confer plant benefits. We provide recommendations on how to mitigate against these negative impacts in modern agriculture.

Survival and Growth of Epiphytic Ferns Depend on Resource Sharing

Locally available resources can be shared within clonal plant systems through physiological integration, thus enhancing their survival and growth. Most epiphytes exhibit clonal growth habit, but few studies have tested effects of physiological integration (resource sharing) on survival and growth of epiphytes and whether such effects vary with species. We conducted two experiments, one on individuals (single ramets) and another on groups (several ramets within a plot), with severed and intact rhizome treatments (without and with physiological integration) on two dominant epiphytic ferns (Polypodiodes subamoena and Lepisorus scolopendrium) in a subtropical montane moist forest in Southwest China. Rhizome severing (preventing integration) significantly reduced ramet survival in the individual experiment and number of surviving ramets in the group experiment, and it also decreased biomass of both species in both experiments. However, the magnitude of such integration effects did not vary significantly between the two species. We conclude that resource sharing may be a general strategy for clonal epiphytes to adapt to forest canopies where resources are limited and heterogeneously distributed in space and time.

Higher clonal integration in the facultative epiphytic fern Selliguea griffithiana growing in the forest canopy compared with the forest understorey

BACKGROUND AND AIMS

The advantage of clonal integration (resource sharing between connected ramets of clonal plants) varies and a higher degree of integration is expected in more stressful and/or more heterogeneous habitats. Clonal facultative epiphytes occur in both forest canopies (epiphytic habitats) and forest understories (terrestrial habitats). Because environmental conditions, especially water and nutrients, are more stressful and heterogeneous in the canopy than in the understorey, this study hypothesizes that clonal integration is more important for facultative epiphytes in epiphytic habitats than in terrestrial habitats.

METHODS

In a field experiment, an examination was made of the effects of rhizome connection (connected vs. disconnected, i.e. with vs. without clonal integration) on survival and growth of single ramets, both young and old, of the facultative epiphytic rhizomatous fern Selliguea griffithiana (Polypodiaceae) in both epiphytic and terrestrial habitats. In another field experiment, the effects of rhizome connection on performance of ramets were tested in small (10 × 10 cm(2)) and large (20 × 20 cm(2)) plots in both epiphytic and terrestrial habitats.

KEY RESULTS

Rhizome disconnection significantly decreased survival and growth of S. griffithiana in both experiments. The effects of rhizome disconnection on survival of single ramets and on ramet number and growth in plots were greater in epiphytic habitats than in terrestrial habitats.

CONCLUSIONS

Clonal integration contributes greatly to performance of facultative epiphytic ferns, and the effects were more important in forest canopies than in forest understories. The results therefore support the hypothesis that natural selection favours genotypes with a higher degree of integration in more stressful and heterogeneous environments.

QTL analysis of intraspecific differences between two Silene vulgaris ecotypes

BACKGROUND AND AIMS

Serpentine soils provide a highly selective substrate for plant colonization and growth and represent an ideal system for studying the evolution of plant-ecotypes. In the present study the aim was to identify the genetic architecture of morphological traits distinguishing serpentine and non-serpentine ecotypes of Silene vulgaris.

METHODS

Using an F(2) mapping population derived from an intraspecific cross between a serpentine and a non-serpentine ecotype of S. vulgaris, the genetic architecture of 12 morphological traits was explored using a quantitative trait locus (QTL) analysis.

KEY RESULTS

The QTL analysis identified a total of 49 QTLs, of which 24 were classified as major QTLs. The mean number of QTLs per trait category was found to correspond well with numbers reported in the literature for similar crosses. Clustering of QTLs for different traits was found on several linkage groups.

CONCLUSIONS

Morphological traits that differentiate the two ecotypes are strongly correlated, presumably as a consequence of the joint effects of extensive linkage of QTLs for different traits and directional selection. The signature of consistent directional selection was found for leaf and shoot trait divergence. Intraspecific ecotype differences in S. vulgaris were found to be distributed across the entire genome. The study shows that QTL analyses on non-model organisms can provide novel insights into the genetic basis of plant diversification.