Fire transforms effects of terrestrial subsidies on aquatic ecosystem structure and function.

Fire can lead to transitions between forest and grassland ecosystems and trigger positive feedbacks to climate warming by releasing CO2 into the atmosphere. Climate change is projected to increase the prevalence and severity of wildfires. However, fire effects on the fate and impact of terrestrial organic matter (i.e., terrestrial subsidies) in aquatic ecosystems are unclear. Here, we performed a gradient design experiment in freshwater pond mesocosms adding 15 different amounts of burned or unburned plant detritus and tracking the chronology of detritus effects at 10, 31, 59, and 89 days. We show terrestrial subsidies had time- and mass-dependent, non-linear impacts on ecosystem function that influenced dissolved organic carbon (DOC), ecosystem metabolism (net primary production and respiration), greenhouse gas concentrations (carbon dioxide [CO2 ], methane [CH4 ]), and trophic transfer. These impacts were shifted by fire treatment. Burning increased the elemental concentration of detritus (increasing %N, %P, %K), with cascading effects on ecosystem function. Mesocosms receiving burned detritus had lower [DOC] and [CO2 ] and higher dissolved oxygen (DO) through Day 59. Fire magnified the effects of plant detritus on aquatic ecosystem metabolism by stimulating photosynthesis and respiration at intermediate detritus-loading through Day 89. The effect of loading on DO was similar for burned and unburned treatments (Day 10); however, burned-detritus in the highest loading treatments led to sustained hypoxia (through Day 31), and long-term destabilization of ecosystem metabolism through Day 89. In addition, fire affected trophic transfer by increasing autochthonous nitrogen source utilization and reducing the incorporation of 15 N-labeled detritus into plankton biomass, thereby reducing the flux of terrestrial subsidies to higher trophic levels. Our results indicate fire chemically transforms plant detritus and alters the role of aquatic ecosystems in processing and storing carbon. Wildfire may therefore induce shifts in ecosystem functions that cross the boundary between aquatic and terrestrial habitats.

Intraspecific variation in leaf litter alters fitness metrics and the gut microbiome of consumers.

Biodiversity can have cascading effects throughout ecosystems. While these effects are better understood at coarser taxonomic scales of biodiversity, there has been a resurgence in investigating how biodiversity within species may have cascading effects on communities and ecosystems. We investigate the broader trophic implications of intraspecific variation in the riparian tree, Alnus rubra, where immediately local or 'home' litter decomposes faster than 'away' litter in aquatic and terrestrial systems. With climate change shifting the distributions of plants across the globe, it is essential to understand how shifts in the intraspecific traits of leaf litter may have reverberating effects throughout ecosystems. Here, we find that intraspecific variation in leaf litter has fitness implications for invertebrate consumers, including the algivorous Dicosmoecus and detrivorous Psychoglypha caddisflies, which exhibited increased body size and muscle nitrogen content when incubated within in-situ river mesocosms supplied with local A. rubra litter. Litter source altered caddisfly gut microbiomes by increasing relative abundance of methanogens and methanotrophs among the non-local treatment group. Additionally, Dicosmoecus supplied with non-local litter may have shifted their diet towards a higher proportion of algae, as inferred from shifts in gut microbiome composition and isotopic ratios of muscle tissue. Overall, our study demonstrates that shifting distributions of plant genotypes across the globe may cause plant-microbe mismatches that will disrupt patterns of decomposition and may have consequences on the fitness and foraging behavior of consumers.

Genome evolution and host-microbiome shifts correspond with intraspecific niche divergence within harmful algal bloom-forming Microcystis aeruginosa.

Intraspecific niche divergence is an important driver of species range, population abundance and impacts on ecosystem functions. Genetic changes are the primary focus when studying intraspecific divergence; however, the role of ecological interactions, particularly host-microbiome symbioses, is receiving increased attention. The relative importance of these evolutionary and ecological mechanisms has seen only limited evaluation. To address this question, we used Microcystis aeruginosa, the globally distributed cyanobacterium that dominates freshwater harmful algal blooms. These blooms have been increasing in occurrence and intensity worldwide, causing major economic and ecological damages. We evaluated 46 isolates of M. aeruginosa and their microbiomes, collected from 14 lakes in Michigan, USA, that vary over 20-fold in phosphorus levels, the primary limiting nutrient in freshwater systems. Genomes of M. aeruginosa diverged along this phosphorus gradient in genomic architecture and protein functions. Fitness in low-phosphorus lakes corresponded with additional shifts within M. aeruginosa including genome-wide reductions in nitrogen use, an expansion of phosphorus assimilation genes and an alternative life history strategy of nonclonal colony formation. In addition to host shifts, despite culturing in common-garden conditions, host-microbiomes diverged along the gradient in taxonomy, but converged in function with evidence of metabolic interdependence between the host and its microbiome. Divergence corresponded with a physiological trade-off between fitness in low-phosphorus environments and growth rate in phosphorus-rich conditions. Co-occurrence of genotypes adapted to different nutrient environments in phosphorus-rich lakes may have critical implications for understanding how M. aeruginosa blooms persist after initial nutrient depletion. Ultimately, we demonstrate that the intertwined effects of genome evolution, host life history strategy and ecological interactions between a host and its microbiome correspond with an intraspecific niche shift with important implications for whole ecosystem function.

Ecological Engineering Helps Maximize Function in Algal Oil Production.

Algal biofuels have the potential to curb the emissions of greenhouse gases from fossil fuels, but current growing methods fail to produce fuels that meet the multiple standards necessary for economical industrial use. For example, algae grown as monocultures for biofuel production have not simultaneously and economically achieved high yields of the high-quality lipid-rich biomass desired for the industrial-scale production of bio-oil. Decades of study in the field of ecology have demonstrated that simultaneous increases in multiple functions, such as the quantity and quality of biomass, can occur in natural ecosystems by increasing biological diversity. Here, we show that species consortia of algae can improve the production of bio-oil, which benefits from both a high biomass yield and a high quality of biomass rich in fatty acids. We explain the underlying causes of increased quantity and quality of algal biomass among species consortia by showing that, relative to monocultures, species consortia can differentially regulate lipid metabolism genes while growing to higher levels of biomass, in part due to a greater utilization of nutrient resources. We identify multiple genes involved in lipid biosynthesis that are frequently upregulated in bicultures and further show that these elevated levels of gene expression are highly predictive of the elevated levels in biculture relative to that in monoculture of multiple quality metrics of algal biomass. These results show that interactions between species can alter the expression of lipid metabolism genes and further demonstrate that our understanding of diversity-function relationships from natural ecosystems can be harnessed to improve the production of bio-oil.IMPORTANCE Algal biofuels are one of the more promising forms of renewable energy. In our study, we investigate whether ecological interactions between species of microalgae regulate two important factors in cultivation-the biomass of the crop produced and the quality of the biomass that is produced. We found that species interactions often improved production yields, especially the fatty acid content of the algal biomass, and that differentially expressed genes involved in fatty acid metabolism are predictive of improved quality metrics of bio-oil. Other studies have found that diversity often improves productivity and stability in agricultural and natural ecosystems. Our results provide further evidence that growing multispecies crops of microalgae may improve the production of high-quality biomass for bio-oil.

Inducible phenotypic plasticity in plants regulates aquatic ecosystem functioning.

Differences among individuals within species affect community and ecosystem processes in many systems, and may rival the importance of differences between species. Intraspecific variation consists of both plastic and genetic components that are regulated by different processes and operate on different time scales. Therefore, probing which mechanisms can affect traits sufficiently strongly to affect ecosystem processes is fundamental to understanding the consequences of individual variation. We find that a dominant deciduous tree of Pacific Northwest riparian ecosystems, red alder, exhibits strong and synergistic responses to nutrient resources and herbivory stress. These induced responses, which include shifting nutrient and plant secondary metabolite composition, have cascading effects on aquatic ecosystem function. Defense responses suppress leaf litter decomposition in small streams, thus altering the rate of energy capture for one of the most abundant terrestrial carbon sources entering aquatic systems. We find that alder responses to herbivory stress largely depend on availability of soil nutrients, with modification of the highly cytotoxic diarylheptanoid group of secondary metabolites being favored in nutrient-poor environments and modification of the typically dose-dependent ellagitannins being favored in nutrient-rich environments. Importantly, these findings identify traits for herbivore resistance in alder trees and demonstrate that plastic responses occurring within a species and over short time scales substantially alter a key function of an adjacent ecosystem. Furthermore, demonstrating plasticity among alder secondary metabolites lends insight into this system, in which decomposer communities are known to adjust to the secondary chemistry of local alder trees to facilitate rapid decomposition of locally derived leaf litter.

Intraspecific leaf chemistry drives locally accelerated ecosystem function in aquatic and terrestrial communities.

Resource patchiness influences consumer foraging, movement, and physiology. Fluxes across ecosystem boundaries can extend these effects to otherwise distinct food webs. Intraspecific diversity of these cross-ecosystem subsidies can have large consequences for recipient systems. Here, we show intraspecific variation in leaf defensive chemistry of riparian trees drives local adaptation among terrestrial and riverine decomposers that consume shed leaf litter. We found extensive geographic structuring of ellagitannins, diarylheptanoids, and flavonoids in red alder trees. Ellagitannins, particularly those with strong oxidative activity, drive aquatic leaf decomposition. Further, spatial variation in these leaf components drives local ecological matching: in experiments using artificial food sources distinguished only by the chemical content of individual trees, we found decomposers both on land and in rivers more quickly consumed locally derived food sources. These results illustrate that terrestrial processes can change the chemistry of cross-ecosystem subsidies in ways that ultimately alter ecosystem function in donor and recipient systems.

Cascading effects of induced terrestrial plant defences on aquatic and terrestrial ecosystem function.

Herbivores induce plants to undergo diverse processes that minimize costs to the plant, such as producing defences to deter herbivory or reallocating limited resources to inaccessible portions of the plant. Yet most plant tissue is consumed by decomposers, not herbivores, and these defensive processes aimed to deter herbivores may alter plant tissue even after detachment from the plant. All consumers value nutrients, but plants also require these nutrients for primary functions and defensive processes. We experimentally simulated herbivory with and without nutrient additions on red alder (Alnus rubra), which supplies the majority of leaf litter for many rivers in western North America. Simulated herbivory induced a defence response with cascading effects: terrestrial herbivores and aquatic decomposers fed less on leaves from stressed trees. This effect was context dependent: leaves from fertilized-only trees decomposed most rapidly while leaves from fertilized trees receiving the herbivory treatment decomposed least, suggesting plants funnelled a nutritionally valuable resource into enhanced defence. One component of the defence response was a decrease in leaf nitrogen leading to elevated carbon : nitrogen. Aquatic decomposers prefer leaves naturally low in C : N and this altered nutrient profile largely explains the lower rate of aquatic decomposition. Furthermore, terrestrial soil decomposers were unaffected by either treatment but did show a preference for local and nitrogen-rich leaves. Our study illustrates the ecological implications of terrestrial herbivory and these findings demonstrate that the effects of selection caused by terrestrial herbivory in one ecosystem can indirectly shape the structure of other ecosystems through ecological fluxes across boundaries.

Local adaptation of stream communities to intraspecific variation in a terrestrial ecosystem subsidy.

Cross-ecosystem fluxes can intertwine otherwise disparate food webs, but the effects of biodiversity at the genotypic level on fluxes across ecosystems boundaries is not known. Fresh leaves, which vary in traits such as defensive compounds against terrestrial herbivores, drop off trees and enter streams, providing a vital resource for riverine organisms. We demonstrate substantial variation in decomposition rates among individual trees in four different rivers in the Olympic Peninsula of Washington State, USA. We show that locally derived red alder leaf litter decomposes on average 24% faster than red alder leaf litter introduced from other riparian zones. Within rivers, leaves downstream of their parent trees decompose nearly as quickly as leaves from local trees. Leaves upstream of the parent tree decomposed as slowly as leaves from trees growing alongside different rivers. Over time, aquatic decomposer communities have locally adapted to the specific trees supplying the riparian subsidies. In energy-limited environments, such as small shaded streams, consumers must be efficient foragers. Our results indicate that this pressure for efficiency has led to adaptation at a particularly fine scale. More broadly, these results illustrate how genetic diversity and the effects of selection in one ecosystem can indirectly shape the structure of other ecosystems through ecological fluxes across boundaries.

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

Selection for oligotrophy among bacteria inhabiting host microbiomes.

IMPORTANCE: Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.

Effects of Phycosphere Bacteria on Their Algal Host Are Host Species-Specific and Not Phylogenetically Conserved.

Phytoplankton is fundamental to life on Earth. Their productivity is influenced by the microbial communities residing in the phycosphere surrounding algal cells. Expanding our knowledge on how algal-bacterial interactions affect algal growth to more hosts and bacteria can help elucidate general principles of algal-host interactions. Here, we isolated 368 bacterial strains from phycosphere communities, right after phycosphere recruitment from pond water and after a month of lab cultivation and examined their impacts on growth of five green algal species. We isolated both abundant and rare phycosphere members, representing 18.4% of the source communities. Positive and neutral effects predominated over negative effects on host growth. The proportion of each effect type and whether the day of isolation mattered varied by host species. Bacteria affected algal carrying capacity more than growth rate, suggesting that nutrient remineralization and toxic byproduct metabolism may be a dominant mechanism. Across-host algal fitness assays indicated host-specific growth effects of our isolates. We observed no phylogenetic conservation of the effect on host growth among bacterial isolates. Even isolates with the same ASV had divergent effects on host growth. Our results emphasize highly specific host-bacterial interactions in the phycosphere and raise questions as to which mechanisms mediate these interactions.

Host specificity of microbiome assembly and its fitness effects in phytoplankton.

Insights into symbiosis between eukaryotic hosts and their microbiomes have shifted paradigms on what determines host fitness, ecology, and behavior. Questions remain regarding the roles of host versus environment in shaping microbiomes, and how microbiome composition affects host fitness. Using a model system in ecology, phytoplankton, we tested whether microbiomes are host-specific, confer fitness benefits that are host-specific, and remain conserved in time in their composition and fitness effects. We used an experimental approach in which hosts were cleaned of bacteria and then exposed to bacterial communities from natural environments to permit recruitment of microbiomes. We found that phytoplankton microbiomes consisted of a subset of taxa recruited from these natural environments. Microbiome recruitment was host-specific, with host species explaining more variation in microbiome composition than environment. While microbiome composition shifted and then stabilized over time, host specificity remained for dozens of generations. Microbiomes increased host fitness, but these fitness effects were host-specific for only two of the five species. The shifts in microbiome composition over time amplified fitness benefits to the hosts. Overall, this work solidifies the importance of host factors in shaping microbiomes and elucidates the temporal dynamics of microbiome compositional and fitness effects.

Linking snake habitat use to nest predation risk in grassland birds: the dangers of shrub cover.

Extremes in rangeland management, varying from too-frequent fire and intensive grazing to the suppression of both, threaten rangeland ecosystems worldwide. Intensive fire and grazing denude and homogenize vegetation whereas their suppression increases woody cover. Although habitat loss is implicated in grassland bird declines, degradation through intensive management or neglect also decreases breeding habitat and may reduce nesting success through increased rates of nest predation. Snakes are important nest predators, but little is known about how habitat use in snakes relates to predation risk for grassland birds nesting within tallgrass prairie subjected to different grazing and fire frequencies. We evaluated nest survival in the context of habitat used by nesting songbirds and two bird-eating snakes, the eastern yellowbelly racer Coluber constrictor flaviventris and Great Plains ratsnake Pantherophis emoryi. Daily nest survival rates decreased with increasing shrub cover and decreasing vegetation height, which characterize grasslands that have been neglected or intensively managed, respectively. Discriminant function analysis revealed that snake habitats were characterized by higher shrub cover, whereas successful nests were more likely to occur in areas with tall grass and forbs but reduced shrub cover. Because snakes often use shrub habitat, birds nesting in areas with increased shrub cover may be at higher risk of nest predation by snakes in addition to other predators known to use shrub habitat (e.g., mid-sized carnivores and avian predators). Depredated nests also occurred outside the discriminant space of the snakes, indicating that other predators (e.g., ground squirrels Spermophilus spp. and bullsnakes Pituophis catenifer) may be important in areas with denuded cover. Targeted removal of shrubs may increase nest success by minimizing the activity of nest predators attracted to shrub cover.

Microbiomes Reduce Their Host's Sensitivity to Interspecific Interactions.

Bacteria associated with eukaryotic hosts can affect host fitness and trophic interactions between eukaryotes, but the extent to which bacteria influence the eukaryotic species interactions within trophic levels that modulate biodiversity and species coexistence is mostly unknown. Here, we used phytoplankton, which are a classic model for evaluating interactions between species, grown with and without associated bacteria to test whether the bacteria alter the strength and type of species interactions within a trophic level. We demonstrate that host-associated bacteria alter host growth rates and carrying capacity. This did not change the type but frequently changed the strength of host interspecific interactions by facilitating host growth in the presence of an established species. These findings indicate that microbiomes can regulate their host species' interspecific interactions. As between-species interaction strength impacts their ability to coexist, our findings show that microbiomes have the potential to modulate eukaryotic species diversity and community composition.IMPORTANCE Description of the Earth's microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

Genotype and host microbiome alter competitive interactions between Microcystis aeruginosa and Chlorella sorokiniana.

Cyanobacterial harmful algal blooms (cyanoHABs) continue to increase in frequency and magnitude, threatening global freshwater ecosystems and services. In north-temperate lakes cyanobacteria appear in early summer, succeeding green algae as the dominant phytoplankton group, a pattern thought to be mediated by changes in temperature and bioavailable nutrients. To understand additional drivers of this successional pattern our study used reciprocal invasion experiments to examine the competitive interaction between Microcystis aeruginosa, a dominant contributor to cyanoHABs, and the green alga Chlorella sorokiniana. We considered two factors that may impact these interactions: (1) strain variation, with a specific emphasis on the presence or absence of the gene for the hepatotoxin microcystin, and (2) host-associated bacteria. We used toxic M. aeruginosa PCC 7806 (microcystin producing strain), a non-toxic mutant of PCC 7806, non-toxic M. aeruginosa PCC 9701 (non-microcystin producing strain), and C. sorokiniana. Each organism was available free of all bacteria (i.e., axenic) and with a re-introduced defined bacterial community to generate their xenic counterparts. Competitive interactions were assessed with reciprocal invasion experiments between paired xenic and paired axenic populations of C. sorokiniana and one of the two Microcystis strains, each assessed separately. Flow cytometry and random forest models were used to rapidly discriminate and quantify phytoplankton population densities with 99% accuracy. We found that M. aeruginosa PCC 7806, but not strain PCC 9701, could proliferate from low abundance in a steady-state population of C. sorokiniana. Further, the presence of bacteria allowed M. aeruginosa PCC 7806 to grow to a higher population density into an established C. sorokiniana population than when grown axenic. Conversely, when M. aeruginosa was dominant, C. sorokiniana was only able to proliferate from low density into the PCC 9701 strain, and only when axenic. The mutant of PCC 7806 lacking the ability to produce microcystin behaved similarly to the toxic wild-type, implying microcystin is not responsible for the difference in competitive abilities observed between the two wild-type strains. Quantification of microcystins (MCs) when PCC 7806 M. aeruginosa was introduced into the C. sorokiniana culture showed two-fold more MCs per cell when host-associated bacteria were absent compared to present in both species cultures. Our results show that the ability of M. aeruginosa to compete with C. sorokiniana is determined by genomic differences beyond genes involved in microcystin toxin generation and indicate an important role of host-associated bacteria in mediating phytoplankton interspecies interactions. These results expand our understanding of the key drivers of phytoplankton succession and the establishment and persistence of freshwater harmful cyanobacterial blooms.

The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition.

Intraspecific variation in plant nutrient and defensive traits can regulate ecosystem-level processes, such as decomposition and transformation of plant carbon and nutrients. Understanding the regulatory mechanisms of ecosystem functions at local scales may facilitate predictions of the resistance and resilience of these functions to change. We evaluated how riverine bacterial community assembly and predicted gene content corresponded to decomposition rates of green leaf inputs from red alder trees into rivers of Washington State, USA. Previously, we documented accelerated decomposition rates for leaves originating from trees growing adjacent to the site of decomposition versus more distant locales, suggesting that microbes have a "home-field advantage" in decomposing local leaves. Here, we identified repeatable stages of bacterial succession, each defined by dominant taxa with predicted gene content associated with metabolic pathways relevant to the leaf characteristics and course of decomposition. "Home" leaves contained bacterial communities with distinct functional capacities to degrade aromatic compounds. Given known spatial variation of alder aromatics, this finding helps explain locally accelerated decomposition. Bacterial decomposer communities adjust to intraspecific variation in leaves at spatial scales of less than a kilometer, providing a mechanism for rapid response to changes in resources such as range shifts among plant genotypes. Such rapid responses among bacterial communities in turn may maintain high rates of carbon and nutrient cycling through aquatic ecosystems.IMPORTANCE Community ecologists have traditionally treated individuals within a species as uniform, with individual-level biodiversity rarely considered as a regulator of community and ecosystem function. In our study system, we have documented clear evidence of within-species variation causing local ecosystem adaptation to fluxes across ecosystem boundaries. In this striking pattern of a "home-field advantage," leaves from individual trees tend to decompose most rapidly when immediately adjacent to their parent tree. Here, we merge community ecology experiments with microbiome approaches to describe how bacterial communities adjust to within-species variation in leaves over spatial scales of less than a kilometer. The results show that bacterial community compositional changes facilitate rapid ecosystem responses to environmental change, effectively maintaining high rates of carbon and nutrient cycling through ecosystems.

Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery.

Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal-associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast-blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14-bp sequence in the Proteobacteria that matches the 17-bp chloroplast-blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14-bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle-blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n-mer oligonucleotides of each PNA sequence.

Diversity of Riparian Plants among and within Species Shapes River Communities.

Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to alder, local intraspecific differences via decomposition, algal or invertebrate metrics were not observed consistently among maples. These results emphasize that biodiversity of riparian subsidies at the within and across species scale have the potential to affect aquatic ecosystems, although there are complex species-specific effects.