No abstract

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria.

Vector-borne microbes necessarily co-occur with their hosts and vectors, but the degree to which they share common evolutionary or biogeographic histories remains unexplored. We examine the congruity of the evolutionary and biogeographic histories of the bacterium and vector of the Lyme disease system, the most prevalent vector-borne disease in North America. In the eastern and midwestern US, Ixodes scapularis ticks are the primary vectors of Borrelia burgdorferi, the bacterium that causes Lyme disease.

Simultaneous or sequential attack by herbivores and microbes is common in plants. Many seed plants exhibit a defence trade-off against chewing herbivorous insects and leaf-colonizing ('phyllosphere') bacteria, which arises from cross-talk between the phytohormones jasmonic acid (JA, induced by many herbivores) and salicylic acid (SA, induced by many bacteria). This cross-talk may promote reciprocal susceptibility in plants between phyllosphere bacteria and insect herbivores. In a population of native bittercress (Cardamine cordifolia, Brassicaceae), we tested whether simulating prior damage with JA or SA treatment induced resistance or susceptibility (respectively) to chewing herbivores. In parallel, we conducted culture-dependent surveys of phyllosphere bacteria to test the hypothesis that damage by chewing herbivores correlates positively with bacterial abundance in leaves. Finally, we tested whether bacterial infection induced susceptibility to herbivory by a major chewing herbivore of bittercress, Scaptomyza nigrita (Drosophilidae). Overall, our results suggest that reciprocal susceptibility to herbivory and microbial attack occurs in bittercress. We found that JA treatment reduced and SA treatment increased S. nigrita herbivory in bittercress in the field. Bacterial abundance was higher in herbivore-damaged vs. undamaged leaves (especially Pseudomonas syringae). However, Pedobacter spp. and Pseudomonas fluorescens infections were negatively associated with herbivory. Experimental Pseudomonas spp. infections increased S. nigrita herbivory in bittercress. Thus, plant defence signalling trade-offs can have important ecological consequences in nature that may be reflected in a positive correlation between herbivory and phyllosphere bacterial abundance and diversity. Importantly, the strength and direction of this association varies within and among prevalent bacterial groups.

A. Field studies.A.1. Hormone treatments in the field. Equal numbers of bittercress plots were randomized to receive either mock (control), JA, or SA treatment. One half-plot (patch; figure S1e) within each plot was subsequently randomized to receive the treatment based on the outcome of a single Bernoulli(0.5) trial. We delivered hormone treatments to bittercress patches by spraying 50 mL per patch (1 mM solution of either JA or SA in 0.045% v/v methanol; Sigma-Aldrich) during mid-season prior to substantial herbivory at site EL in 2012 and at site NP in 2013, as previously described (1). For site NP, we treated plots between July 12-15, 2013, and we revisited all plots for herbivory and vegetative trait surveys as well as tissue collections between August 13-18, 2013. At EL, we collected a single leaf from a randomly determined leaf position along each of four stems randomly selected from the 16 stems surveyed per patch. We excluded the top two leaves from sampling, which were generally < 1cm 2 -too small to offer adequate amounts of leaf material for DNA extraction. Leaves along each stem were included irrespective of herbivore damage status. Thus, leaves with herbivore damage in our leaf sample set from EL reflected the leaf-level prevalence of herbivore damage in the EL bittercress population.At site NP, we also measured 16 stems per patch, where four sets of four stems were identified as being closest to the inner corners of a 2 × 2 grid (0.5 m per side) placed in the center of each bittercress patch (figure S1e). We sampled a damaged an undamaged leaf from one of the four stems in each grid square (via randomization) and pooled the excised leaf discs from each into damaged and undamaged tissue pools. Thus, each patch contributed two samples: one containing four leaf discs from undamaged leaves and one containing four leaf discs from damaged leaves. Leaves were snipped from plant stems and held at 4 C for up to 12 h prior to processing in the laboratory.A.2. Sample preparation for bacterial detection. Leaf samples were weighed, surface-sterilized, combined into 1.5 mL microcentrifuge tubes, and flash frozen in liquid nitrogen vapor for subsequent homogenization and DNA extraction. Surface sterilization entailed a 5 s rinse in 95% ethanol, 30 s in 70% ethanol, 30 s in 10% bleach, followed by three 2 minute washes in sterile water. Tissue samples were briefly air-dried on sterilized bench-top (5 min) before being homogenized. Sterilized leaf discs were then homogenized in 2.0 mL microcentrifuge tubes in ∼ 350µL 10 mM MgSO 4 using a TissueLyser (QIAGEN) run at max speed (50 Hz) for up to 60 s. We placed a sterilized 5 mm stainless steal ball within each tube to facilitate tissue disruption.We then extracted DNA from all leaf homogenate using the ThermoFisher PureLink Genomic DNA extraction kit following standard protocols. We eluted DNA in 35 µL of sterile water and shipped 10 µL aliquots to Argonne National Laboratory (ANL) at 4 C. ANL staff then performed PCR amplification of the V4 region of 16S using pu...

No abstract

Herbivorous insects are among the most successful radiations of life. However, we know little about the processes underpinning the evolution of herbivory. We examined the evolution of herbivory in the fly, Scaptomyza flava, whose larvae are leaf miners on species of Brassicaceae, including the widely studied reference plant, Arabidopsis thaliana (Arabidopsis). Scaptomyza flava is phylogenetically nested within the paraphyletic genus Drosophila, and the whole genome sequences available for 12 species of Drosophila facilitated phylogenetic analysis and assembly of a transcriptome for S. flava. A time-calibrated phylogeny indicated that leaf mining in Scaptomyza evolved between 6 and 16 million years ago. Feeding assays showed that biosynthesis of glucosinolates, the major class of antiherbivore chemical defense compounds in mustard leaves, was upregulated by S. flava larval feeding. The presence of glucosinolates in wild-type (WT) Arabidopsis plants reduced S. flava larval weight gain and increased egg–adult development time relative to flies reared in glucosinolate knockout (GKO) plants. An analysis of gene expression differences in 5-day-old larvae reared on WT versus GKO plants showed a total of 341 transcripts that were differentially regulated by glucosinolate uptake in larval S. flava. Of these, approximately a third corresponded to homologs of Drosophila melanogaster genes associated with starvation, dietary toxin-, heat-, oxidation-, and aging-related stress. The upregulated transcripts exhibited elevated rates of protein evolution compared with unregulated transcripts. The remaining differentially regulated transcripts also contained a higher proportion of novel genes than the unregulated transcripts. Thus, the transition to herbivory in Scaptomyza appears to be coupled with the evolution of novel genes and the co-option of conserved stress-related genes.

Laboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 Saccharomyces cerevisiae populations (124 haploid and 81 diploid) for ~10,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.