Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.

Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.

A Symbiotic Approach to Generating Stress Tolerant Crops.

Studies were undertaken to determine if fungal endophytes from plants in stressful habitats could be commercialized to generate climate resilient crop plants. Fungal endophytes were isolated from weedy rice plants and grasses from South Korea and the USA, respectively. Endophytes (Curvularia brachyspora and Fusarium asiaticum) from weedy rice plants from high salt or drought stressed habitats in South Korea conferred salt and drought stress tolerance to weedy rice and commercial varieties reflective of the habitats from which they were isolated. Fungal endophytes isolated from grasses in arid habitats of the USA were identified as Trichoderma harzianum and conferred drought and heat stress tolerance to monocots and eudicots. Two T. harzianum isolates were exposed to UV mutagenesis to derive strains resistant to fungicides in seed treatment plant protection packages. Three strains that collectively had resistance to commonly used fungicides were used for field testing. The three-strain mixture (ThSM3a) increased crop yields proportionally to the level of stress plants experienced with average yields up to 52% under high and 3-5% in low stress conditions. This study demonstrates fungal endophytes can be developed as viable commercial tools for rapidly generating climate resilient crops to enhance agricultural sustainability.

The Chromosome-Scale Genome Resource for Two Endophytic Fusarium species, F. culmorum and F. pseudograminearum.

Genus Fusarium (Ascomycota, Hypocreales, Nectriaceae) includes many economically important plant pathogens that cause devastating diseases of a wide range of crops and trees. Interestingly, there is increasing evidence that some Fusarium species also live as endophytes and benefit plant growth and stress tolerance. In this work, we sequence the whole genomes of endophytic F. culmorum and F. pseudograminearum, isolated from a coastal dunegrass (Leymus mollis), using long-read single-molecule real-time sequencing technology. Their genomes are assembled into four chromosomes and a mitochondrial genome with a total assembly size of 40.05 and 42.90 M, respectively. This resource should not only facilitate functional studies designed to better understand what makes the two Fusarium species such successful plant-beneficial fungi but should also reveal their genome evolution and adaptation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Biodiversity and Abundance of Cultured Microfungi from the Permanently Ice-Covered Lake Fryxell, Antarctica.

In this work, we explore the biodiversity of culturable microfungi from the water column of a permanently ice-covered lake in Taylor Valley, Antarctica from austral field seasons in 2003, 2008 and 2010, as well as from glacial stream input (2010). The results revealed that there was a sharp decline in total culturable fungal abundance between 9 and 11 m lake depth with a concurrent shift in diversity. A total of 29 species were identified from all three water sources with near even distribution between Ascomycota and Basidomycota (15 and 14 respectively). The most abundant taxa isolated from Lake Fryxell in 2008 were Glaciozyma watsonii (59%) followed by Penicillium spp. (10%), both of which were restricted to 9 m and above. Although seven species were found below the chemocline of 11 m in 2008, their abundance comprised only 10% of the total culturable fungi. The taxa of isolates collected from glacial source input streams had little overlap with those found in Lake Fryxell. The results highlight the spatial discontinuities of fungal populations that can occur within connected oligotrophic aquatic habitats.

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity.

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.

Validation of a biofeedback system for wheelchair propulsion training.

This paper describes the design and validation of the OptiPush Biofeedback System, a commercially available, instrumented wheel system that records handrim biomechanics and provides stroke-by-stroke biofeedback and targeting for 11 propulsion variables. Testing of the system revealed accurate measurement of wheel angle (0.02% error), wheel speed (0.06% error), and handrim loads. The maximum errors in static force and torque measurements were 3.80% and 2.05%, respectively. Measured forces were also found to be highly linear (0.985 < slope < 1.011) and highly correlated to the reference forces (r(2) > .998). Dynamic measurements of planar forces (F(x) and F(y)) and axle torque also had low error (-0.96 N to 0.83 N for force and 0.10 Nm to 0.14 Nm for torque) and were highly correlated (r > .986) with expected force and torque values. Overall, the OptiPush Biofeedback System provides accurate measurement of wheel dynamics and handrim biomechanics and may be a useful tool for improving manual wheelchair propulsion.

Characterization of mannitol in Curvularia protuberata hyphae by FTIR and Raman spectromicroscopy.

FTIR and Raman spectromicroscopy were used to characterize the composition of Curvularia protuberata hyphae, and to compare a strain isolated from plants inhabiting geothermal soils with a non-geothermal isolate. Thermal IR source images of hyphae have been acquired with a 64 × 64 element focal plane array detector; single point IR spectra have been obtained with synchrotron source light. In some C. protuberata hyphae, we have discovered the spectral signature of crystalline mannitol, a fungal polyol with complex protective roles. With FTIR-FPA imaging, we have determined that the protein content in cells remains fairly constant throughout the length of a hypha, whereas the mannitol is found at discrete, irregular locations. This is the first direct observation of mannitol in intact fungal hyphae. Since the concentration of mannitol in cells varies with respect to position and is not present in all hyphae, this discovery may be related to habitat adaptation, fungal structure and growth stages.

Symbiotic regulation of plant growth, development and reproduction.

The growth and development of rice (Oryzae sativa) seedlings was shown to be regulated epigenetically by a fungal endophyte. In contrast to un-inoculated (nonsymbiotic) plants, endophyte colonized (symbiotic) plants preferentially allocated resources into root growth until root hairs were well established. During that time symbiotic roots expanded at five times the rate observed in nonsymbiotic plants. Endophytes also influenced sexual reproduction of mature big sagebrush (Artemisia tridentata) plants. Two spatially distinct big sagebrush subspecies and their hybrids were symbiotic with unique fungal endophytes, despite being separated by only 380 m distance and 60 m elevation. A double reciprocal transplant experiment of parental and hybrid plants, and soils across the hybrid zone showed that fungal endophytes interact with the soils and different plant genotypes to confer enhanced plant reproduction in soil native to the endophyte and reduced reproduction in soil alien to the endophyte. Moreover, the most prevalent endophyte of the hybrid zone reduced the fitness of both parental subspecies. Because these endophytes are passed to the next generation of plants on seed coats, this interaction provides a selective advantage, habitat specificity, and the means of restricting gene flow, thereby making the hybrid zone stable, narrow and potentially leading to speciation.

Consequences of a cross slope on wheelchair handrim biomechanics.

OBJECTIVE: To test the hypothesis that pushing on a cross slope leads to increased handrim loading compared with that found on a level surface. DESIGN: Case series. SETTING: Biomechanics laboratory. PARTICIPANTS: Twenty-six manual wheelchair users. INTERVENTION: Subjects pushed their own wheelchairs on a research treadmill set to level, 3 degrees , and 6 degrees cross slopes. Propulsion speed was self-selected for each cross-slope condition. Handrim biomechanics were measured for the downhill wheel, using an instrumented wheelchair wheel and a motion capture system. MAIN OUTCOME MEASURES: Speed, peak kinetics (force, rate of loading, torque), push angle, cadence, push distance, and power output were averaged over a 20-push set for each subject and each cross-slope condition. Outcomes were compared across cross slopes using a repeated-measures analysis of variance. RESULTS: Push angle and cadence were unaffected by cross slope. A trend of decreasing self-selected speeds with increasing cross slope was not significant. There were considerable increases in the peak kinetic measures, with the axial moment increasing by a factor of 1.8 on the 6 degrees cross slope (P=.000). More pushes were required to cover the same distance when on a cross slope (P<.034). The power required for propulsion increased by a factor of 2.3 on the 6 degrees cross slope (P=.000). CONCLUSIONS: Users must push harder when on a cross slope. This increased loading is borne by the users' arms, which are at risk for overuse injuries. Exposure to biomechanic loading can be reduced by avoiding cross slopes when possible.

Stroke pattern and handrim biomechanics for level and uphill wheelchair propulsion at self-selected speeds.

OBJECTIVES: To investigate the natural stroke patterns of wheelchair users pushing on a level surface, to determine if users adapt their stroke patterns for pushing uphill, and to assess whether there are biomechanic advantages to one or more of the stroke patterns. DESIGN: Case series. SETTING: Biomechanics laboratory. PARTICIPANTS: Twenty-six manual wheelchair users with a spinal cord injury. INTERVENTION: Subjects pushed their own wheelchairs at self-selected speeds on a research treadmill set to level, 3 degrees , and 6 degrees grades. Stroke patterns were measured using a motion capture system. Handrim biomechanics were measured using an instrumented wheel. MAIN OUTCOME MEASURES: Stroke patterns were classified for both level and uphill propulsion according to 1 of 4 common classifications: arcing, semi-circular, single-looping (SLOP), and double-looping (DLOP). Biomechanic outcomes of speed, peak handrim force, cadence, and push angle were all compared across stroke classifications using an analysis of variance. RESULTS: Only 3 of the 4 stroke patterns were observed. None of the subjects used the semi-circular pattern. For level propulsion, the stroke patterns were fairly balanced between arcing (42%), SLOP (31%), and DLOP (27%). Subjects tended to change their stroke pattern for pushing uphill, with 73% of the subjects choosing the arcing pattern by the 6 degrees grade. No statistically significant differences were found in handrim biomechanics or subject characteristics across stroke pattern groups. CONCLUSIONS: Wheelchair users likely adapt their stroke pattern to accommodate their propulsion environment. Based on the large percentage of subjects who adopted the arcing pattern for pushing uphill, there may be benefits to the arcing pattern for pushing uphill. In light of this and other recent work, it is recommended that clinicians not instruct users to utilize a single stroke pattern in their everyday propulsion environments.

A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance.

A mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. We characterized a virus from this fungus that is involved in the mutualistic interaction. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants.

Genotype, soil type, and locale effects on reciprocal transplant vigor, endophyte growth, and microbial functional diversity of a narrow sagebrush hybrid zone in Salt Creek Canyon, Utah.

When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F(1) hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F(1) hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden-by-soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F(1) hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.

Reduced finger and wrist flexor activity during propulsion with a new flexible handrim.

OBJECTIVE: To test the hypothesis that finger and wrist flexor activity is lower when pushing with a high-friction flexible handrim than with a standard uncoated handrim. DESIGN: Case series. SETTING: Biomechanics laboratory. PARTICIPANTS: Twenty-four manual wheelchair users. INTERVENTION: Subjects pushed their own wheelchairs on a research treadmill set to level, 3 degrees , and 6 degrees grades using both a standard uncoated handrim and a high friction flexible handrim. Propulsion speed was self-selected and held constant between handrim trials. Handrim order was randomized. Finger and wrist flexor muscle activity was measured at the forearm using surface electromyography. MAIN OUTCOME MEASURES: Electromyographic data were rectified and normalized by each subject's maximum voluntary contraction. Total muscle exertion was determined by integrating the rectified signal over each push. Peak and total muscle exertion for each push were averaged across grade conditions and compared across handrims using a repeated measures t test. RESULTS: The flexible handrim resulted in statistically significant reductions in both peak and total forearm muscle activation. Averaging across all subjects and grade conditions, peak muscle activation was reduced by 11.8% (P=.026) and overall muscle exertion was reduced by 14.5% (P=.016). CONCLUSIONS: The flexible handrim was shown to require less finger and wrist flexor activity than a standard uncoated handrim for the same propulsion conditions.

Spatial partitioning and asymmetric hybridization among sympatric coastal steelhead trout (Oncorhynchus mykiss irideus), coastal cutthroat trout (O. clarki clarki) and interspecific hybrids.

Hybridization between sympatric species provides unique opportunities to examine the contrast between mechanisms that promote hybridization and maintain species integrity. We surveyed hybridization between sympatric coastal steelhead (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki) from two streams in Washington State, Olsen Creek (256 individuals sampled) and Jansen Creek (431 individuals sampled), over a 3-year period. We applied 11 O. mykiss-specific nuclear markers, 11 O. c. clarki-specific nuclear markers and a mitochondrial DNA marker to assess spatial partitioning among species and hybrids and determine the directionality of hybridization. F1 and post-F1 hybrids, respectively, composed an average of 1.2% and 33.6% of the population sampled in Jansen Creek, and 5.9% and 30.4% of the population sampled in Olsen Creek. A modest level of habitat partitioning among species and hybrids was detected. Mitochondrial DNA analysis indicated that all F1 hybrids (15 from Olsen Creek and five from Jansen Creek) arose from matings between steelhead females and cutthroat males implicating a sneak spawning behaviour by cutthroat males. First-generation cutthroat backcrosses contained O. c. clarki mtDNA more often than expected suggesting natural selection against F1 hybrids. More hybrids were backcrossed toward cutthroat than steelhead and our results indicate recurrent hybridization within these creeks. Age analysis demonstrated that hybrids were between 1 and 4 years old. These results suggest that within sympatric salmonid hybrid zones, exogenous processes (environmentally dependent factors) help to maintain the distinction between parental types through reduced fitness of hybrids within parental environments while divergent natural selection promotes parental types through distinct adaptive advantages of parental phenotypes.

Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences.

The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.