Network analysis of nematodes with soil microbes on cool-season golf courses

Nematodes are an active part of complex soil food webs on golf courses, with some members promoting plant growth, while others are pathogenic or neutralists. The artificial, sand-based rootzone mixtures of putting greens, the most intensely managed areas of a golf course, are especially prone to nematode damage. A better understanding of the interactions of nematodes with soil microbes is key to developing improved turf management strategies. The coupling of amplicon sequencing with network analysis provides a way of better understanding which taxa may be closely associated, allowing hypothesis generation to learn more about how nematodes interact with soil microbes. We performed weighted gene correlation network analyses on bacteria, fungi, and bacteria with nematodes and fungi with nematodes collected from the soil of roughs, fairways, and putting greens of three cool-season turfgrass golf courses on Martha\u27s Vineyard, Massachusetts. Rhodoplanes spp. were found in many bacterial modules, suggesting they may be a common species. Many nematodes formed positive correlations with known nematode antagonizing microbes. Among five nematode trophic groups, the carnivorous nematodes were most connected to both bacteria and fungi, suggesting these nematodes may have previously overlooked interactions with soil microbes. Consensus eigengene networks were highly preserved among management areas on each golf course for both the bacteria and fungi, showing conserved meta-modules despite management differences. The results of this work provide deeper insight into a unique, complex perennial ecosystem on golf courses that could be leveraged for future investigations on these relationships and eventually to improved turf health and disease management in the future. To our knowledge this study is the first use of network analysis to explore the relationship of the turf-associated bacterial and fungal phytobiomes with nematodes

Plant origin and ploidy influence gene expression and life cycle characteristics in an invasive weed

Background: Ecological, evolutionary and physiological studies have thus far provided an incomplete picture of why some plants become invasive; therefore we used genomic resources to complement and advance this field. In order to gain insight into the invasive mechanism of Centaurea stoebe we compared plants of three geo-cytotypes, native Eurasian diploids, native Eurasian tetraploids and introduced North American tetraploids, grown in a common greenhouse environment. We monitored plant performance characteristics and life cycle habits and characterized the expression of genes related to constitutive defense and genome stability using quantitative PCR. Results: Plant origin and ploidy were found to have a significant effect on both life cycle characteristics and gene expression, highlighting the importance of comparing appropriate taxonomic groups in studies of native and introduced plant species. We found that introduced populations of C. stoebe exhibit reduced expression of transcripts related to constitutive defense relative to their native tetraploid counterparts, as might be expected based on ideas of enemy release and rapid evolution. Measurements of several vegetative traits were similar for all geo-cytotypes; however, fecundity of tetraploids was significantly greater than diploids, due in part to their polycarpic nature. A simulation of seed production over time predicts that introduced tetraploids have the highest fecundity of the three geo-cytotypes. Conclusion: Our results suggest that characterizing gene expression in an invasive species using populations from both its native and introduced range can provide insight into the biology of plant invasion that can complement traditional measurements of plant performance. In addition, these results highlight the importance of using appropriate taxonomic units in ecological genomics investigations

Ethanol Attracts Scolytid Beetles to Phytophthora ramorum Cankers on Coast Live Oak

Ethanol in sapwood was analyzed along vertical transects, through small spot cankers and larger basal cankers, of Phytophthora ramorum-infected stems of Quercus agrifolia at three sites in California. Trees with large basal cankers, known to attract scolytid beetles, had a 4.3 times higher ethanol level than trees with spot cankers that attract fewer beetles. Ethanol concentrations inside cankers, where scolytid beetles preferentially attack, varied by about four orders of magnitude among samples, with a median level of 16.0 mu g.g(-1) fresh mass. This concentration was 4.3 and 15.5 times greater, respectively, than the concentrations at 1 cm or 15-30 cm outside the canker boundaries. In the laboratory, we demonstrated that ethanol escaped through the bark of a Q. garryana log just 3 days after it was added to the sapwood. At the three study sites, traps baited with ethanol captured more Xyleborinus saxesenii, Pseudopityophthorus pubipennis, and Monarthrum dentiger (all Coleoptera: Curculionidae: Scolytinae) than traps baited with ethanol plus (-)-alpha-pinene, or ethanol plus 4-allylanisole (4AA). Logs of Q. agrifolia with a 50 % ethanol solution added to the sapwood were placed at the study sites, with or without additional bark treatments above the ethanol. The number of scolytid beetle gallery holes above the ethanol-infused sapwood was 4.4 times greater than that on the opposite side of the log where no ethanol was added. Attachment of ultra-high release (-)-alpha-pinene pouches to the bark surface above the 50 % ethanol solution reduced scolytid attacks to a density of 19.1 % that of logs without this treatment. We conclude that ethanol in P. ramorum cankers functions as a primary host attractant for scolytid beetles and is an important link in colonization of these cankers and accelerated mortality of Q. agrifolia. The results of this research shed light on the chemical ecology behind the focused scolytid attacks on P. ramorum-infected coast live oaks, and lay the groundwork for future efforts to prolong the survival of individual trees of this keystone species.Keywords: Ethanol, Quercus agrifolia, Phytophthora ramorum, Deterrents . (−)-α-Pinene, Ambrosia beetles, Sudden oak death, Bark beetles, 4-Allylanisol

Whole Body Mechanics of Stealthy Walking in Cats

The metabolic cost associated with locomotion represents a significant part of an animal's metabolic energy budget. Therefore understanding the ways in which animals manage the energy required for locomotion by controlling muscular effort is critical to understanding limb design and the evolution of locomotor behavior. The assumption that energetic economy is the most important target of natural selection underlies many analyses of steady animal locomotion, leading to the prediction that animals will choose gaits and postures that maximize energetic efficiency. Many quadrupedal animals, particularly those that specialize in long distance steady locomotion, do in fact reduce the muscular contribution required for walking by adopting pendulum-like center of mass movements that facilitate exchange between kinetic energy (KE) and potential energy (PE) [1]–[4]. However, animals that are not specialized for long distance steady locomotion may face a more complex set of requirements, some of which may conflict with the efficient exchange of mechanical energy. For example, the “stealthy” walking style of cats may demand slow movements performed with the center of mass close to the ground. Force plate and video data show that domestic cats (Felis catus, Linnaeus, 1758) have lower mechanical energy recovery than mammals specialized for distance. A strong negative correlation was found between mechanical energy recovery and diagonality in the footfalls and there was also a negative correlation between limb compression and diagonality of footfalls such that more crouched postures tended to have greater diagonality. These data show a previously unrecognized mechanical relationship in which crouched postures are associated with changes in footfall pattern which are in turn related to reduced mechanical energy recovery. Low energy recovery was not associated with decreased vertical oscillations of the center of mass as theoretically predicted, but rather with posture and footfall pattern on the phase relationship between potential and kinetic energy. An important implication of these results is the possibility of a tradeoff between stealthy walking and economy of locomotion. This potential tradeoff highlights the complex and conflicting pressures that may govern the locomotor choices that animals make

Understanding and Enhancing Soil Biological Health: The Solution for Reversing Soil Degradation

Our objective is to provide an optimistic strategy for reversing soil degradation by increasing public and private research efforts to understand the role of soil biology, particularly microbiology, on the health of our world’s soils. We begin by defining soil quality/soil health (which we consider to be interchangeable terms), characterizing healthy soil resources, and relating the significance of soil health to agroecosystems and their functions. We examine how soil biology influences soil health and how biological properties and processes contribute to sustainability of agriculture and ecosystem services. We continue by examining what can be done to manipulate soil biology to: (i) increase nutrient availability for production of high yielding, high quality crops; (ii) protect crops from pests, pathogens, weeds; and (iii) manage other factors limiting production, provision of ecosystem services, and resilience to stresses like droughts. Next we look to the future by asking what needs to be known about soil biology that is not currently recognized or fully understood and how these needs could be addressed using emerging research tools. We conclude, based on our perceptions of how new knowledge regarding soil biology will help make agriculture more sustainable and productive, by recommending research emphases that should receive first priority through enhanced public and private research in order to reverse the trajectory toward global soil degradation

Physiological impacts of Swiss needle cast on Douglas-fir

A series of studies, in three western Oregon Douglas-fir plantations, was conducted to understand the physiological impacts of Swiss needle cast on Douglas-fir physiology. Four aspects of the disease complex were investigated: fungal colonization and assessment, plant-water relations, carbon assimilation and interaction with climate. Several techniques were developed and used to assess the colonization of Phaeocryptopus gaeumannii, the causal fungus, in foliage (i.e., ergosterol concentration, quantitative PCR, and visual estimates of fruiting bodies). All measures of fungal colonization were significantly correlated with each other (r [greater than or equal to] 0.733) and with the amount of visible symptoms present (i.e., needle chlorosis and retention) (r [greater than or equal to] 0.578). Furthermore, removal of P. gaeumannii with fungicide applications reduced visible symptoms and increased tree growth. Upon sporulation, P. gaeumannii produces fruiting bodies (pseudothecia) that emerge from needle stomata, significantly reducing gas exchange in Douglas-fir needles by physically impeding gaseous diffusion. Maximum rates of needle gas exchange (CO₂ and H₂O) were inversely proportional to the presence of P. gaeurnannii in needle stomata. Anatomical and biochemical changes, such as reduced sapwood permeability and reduced rubisco activity, associated with prolonged disease presence further reduced the capacity and duration of needle gas exchange. Climate was also shown to play a significant role in disease development. Differences associated with site topography (i.e., slope and aspect), influenced both fungal colonization and symptom development. For example, an increase in fungal colonization and symptom development was observed on foliage from south slopes, which typically experienced greater evaporative demands (i.e., increased temperature and/or 1ower relative humidity). The cumulative effects of P. gaeumannii infection were integrated into a process-based model of photosynthesis. Modeled estimates of stomatal conductance and photosynthesis were well correlated with observed values (R²= 0.777, R² = 0.820, respectively). Yearly estimates of whole-canopy carbon assimilation, accounting for P. gaeumannii infection and site climate differences, were significantly correlated with tree height growth (R² = 0.792)

Reviewing the Current Understanding of Replant Syndrome in Orchards from a Soil Microbiome Perspective

Replant syndrome (RS) of fruit and nut trees causes reduced tree vigor and crop productivity in orchard systems due to repeated plantings of closely related tree species. Although RS etiology has not been clearly defined, the causal agents are thought to be a complex of soil microorganisms combined with abiotic factors and susceptible tree genetics. Different soil disinfection techniques alleviate RS symptoms by reducing the loads of the deleterious microbiome; however, the positive effect on crop growth is temporary. The goals of this paper are: (1) to conceptualize the establishment of the syndrome from a microbiome perspective and (2) to propose sustainable solutions to develop a beneficial microbiome to inhibit the onset of RS

Negative Effects of Sample Pooling on PCR-Based Estimates of Soil Microbial Richness and Community Structure ▿ †

In this study, we examined the effect of various pooling strategies on the characterization of soil microbial community composition and phylotype richness estimates. Automated ribosomal intergenic spacer analysis (ARISA) profiles were determined from soil samples that were (i) unpooled (extracted and amplified individually), (ii) pooled prior to PCR amplification, or (iii) pooled prior to DNA extraction. Regression analyses suggest that the less even the soil microbial community (i.e., low Shannon equitability, EH), the greater was the impact of either pooling strategy on microbial detection (R2 = 0.766). For example, at a tropical rainforest site, which had the most uneven fungal (EH of 0.597) and bacterial communities (EH of 0.822), the unpooled procedure detected an additional 67 fungal and 115 bacterial phylotypes relative to either of the pooled procedures. Phylotype rarity, resulting in missed detection upon pooling, differed between the fungal and bacterial communities. Fungi were typified by locally abundant but spatially rare phylotypes, and the bacteria were typified by locally rare but spatially ubiquitous phylotypes. As a result, pooling differentially influenced plot comparisons, leading to an increase in similarity for the bacterial community and a decrease in the fungal community. In conclusion, although pooling reduces sample numbers and variability, it could mask a significant portion of the detectable microbial community, particularly for fungi due to their higher spatial heterogeneity

Pairwise comparison between values of Shannon’s alpha diversity assigned to each treatment.

(Above) Comparison of Shannon’s α-diversity values between disrupted and undisrupted treatments. (Below) Comparison of Shannon’s α-diversity values between communities detected in disrupted no plant treatments and disrupted plant treatments (e.g. Crop: Autoclaved = disrupted, Crop: Unautoclaved = undisrupted). (XLSX)</p