Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors.

Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.

Functional trait trade-offs define plant population stability across different biomes.

Ecological theory posits that temporal stability patterns in plant populations are associated with differences in species' ecological strategies. However, empirical evidence is lacking about which traits, or trade-offs, underlie species stability, especially across different biomes. We compiled a worldwide collection of long-term permanent vegetation records (greater than 7000 plots from 78 datasets) from a large range of habitats which we combined with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits. We found that populations with greater leaf dry matter content and seed mass were more stable over time. Despite the variability explained by these traits being low, their effect was consistent across different datasets. Other traits played a significant, albeit weaker, role in species stability, and the inclusion of multi-variate axes or phylogeny did not substantially modify nor improve predictions. These results provide empirical evidence and highlight the relevance of specific ecological trade-offs, i.e. in different resource-use and dispersal strategies, for plant populations stability across multiple biomes. Further research is, however, necessary to integrate and evaluate the role of other specific traits, often not available in databases, and intraspecific trait variability in modulating species stability.

Climate and plant community diversity in space and time.

Climate strongly shapes plant diversity over large spatial scales, with relatively warm and wet (benign, productive) regions supporting greater numbers of species. Unresolved aspects of this relationship include what causes it, whether it permeates to community diversity at smaller spatial scales, whether it is accompanied by patterns in functional and phylogenetic diversity as some hypotheses predict, and whether it is paralleled by climate-driven changes in diversity over time. Here, studies of Californian plants are reviewed and new analyses are conducted to synthesize climate-diversity relationships in space and time. Across spatial scales and organizational levels, plant diversity is maximized in more productive (wetter) climates, and these consistent spatial relationships are mirrored in losses of taxonomic, functional, and phylogenetic diversity over time during a recent climatic drying trend. These results support the tolerance and climatic niche conservatism hypotheses for climate-diversity relationships, and suggest there is some predictability to future changes in diversity in water-limited climates.

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions.

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.

Synchrony matters more than species richness in plant community stability at a global scale.

The stability of ecological communities is critical for the stable provisioning of ecosystem services, such as food and forage production, carbon sequestration, and soil fertility. Greater biodiversity is expected to enhance stability across years by decreasing synchrony among species, but the drivers of stability in nature remain poorly resolved. Our analysis of time series from 79 datasets across the world showed that stability was associated more strongly with the degree of synchrony among dominant species than with species richness. The relatively weak influence of species richness is consistent with theory predicting that the effect of richness on stability weakens when synchrony is higher than expected under random fluctuations, which was the case in most communities. Land management, nutrient addition, and climate change treatments had relatively weak and varying effects on stability, modifying how species richness, synchrony, and stability interact. Our results demonstrate the prevalence of biotic drivers on ecosystem stability, with the potential for environmental drivers to alter the intricate relationship among richness, synchrony, and stability.

Extreme pre-fire drought decreases shrub regeneration on fertile soils.

Extreme drought and increasing temperatures can decrease the resilience of plant communities to fires. Not only may extremely dry conditions during or after fires lead to higher plant mortality and poorer recruitment, but severe pre-fire droughts may reduce the seed production and belowground vigor that are essential to post-fire plant recovery, and may indirectly facilitate invasion. We studied survival, recruitment, and growth of shrubs and herbs in chaparral (shrubland) communities in Northern California after a 2015 fire that immediately followed California's extreme 3-yr drought. We followed the same protocols used to study similar, adjacent communities after a 1999 fire that did not follow a drought, and we compared the two recovery trajectories. Overall, the 2015 fire was not more severe than the 1999 fire, yet it caused higher mortality and lower growth of resprouting shrubs on fertile (sandstone) soils. In contrast, the 2015 fire did not affect the mortality or growth of resprouting shrubs on infertile (serpentine) soils, the density of shrub seedlings, or the richness or cover of native herbs differently than the 1999 fire. However, the 2015 fire facilitated a massive increase in exotic herbaceous cover, especially on fertile soils, possibly portending the early stages of a type conversion to exotic-dominated grassland. Our findings indicate that the consequences of climate change on fire-dependent communities will include effects of pre-fire as well as post-fire climate, and that resprouting shrubs are particularly likely to be sensitive to pre-fire drought.

Seedling traits predict drought-induced mortality linked to diversity loss.

Trait-based approaches are increasingly used to predict ecological consequences of climate change, yet seldom have solid links been established between plant traits and observed climate-driven community changes. Most analyses have focused on aboveground adult plant traits, but in warming and drying climates, root traits may be critical, and seedlings may be the vulnerable stage. Relationships of seedling and root traits to more commonly measured traits and ecological outcomes are poorly known. In an annual grassland where winter drought-induced seedling mortality is driving a long-term decline in native diversity, using a field experiment during the exceptionally dry winter of 2017-2018, we found that seedling mortality was higher and growth of seedlings and adults were lower in unwatered than watered sites. Mortality of unwatered seedlings was higher in species with shorter seedling roots, and also in species with the correlated traits of small seeds, high seedling specific leaf area (SLA), and tall seedlings. Adult traits varied along an axis from short-stature, high SLA and foliar N, and early flowering to the opposite values, and were only weakly correlated with seedling traits and seedling mortality. No evidence was found for adaptive plasticity, such as longer roots or lower SLA in unwatered plants. Among these species, constitutive variation in seedling root length explained most of the variation in survival of a highly vulnerable life stage under winter drought. Selective loss of species with high adult SLA, observed in this community and others under drought stress, may be the byproduct of other correlated traits.

Climate drives loss of phylogenetic diversity in a grassland community.

While climate change has already profoundly influenced biodiversity through local extinctions, range shifts, and altered interactions, its effects on the evolutionary history contained within sets of coexisting species-or phylogenetic community diversity-have yet to be documented. Phylogenetic community diversity may be a proxy for the diversity of functional strategies that can help sustain ecological systems in the face of disturbances. Under climatic warming, phylogenetic diversity may be especially vulnerable to decline in plant communities in warm, water-limited regions, as intensified water stress eliminates drought-intolerant species that may be relicts of past wetter climates and may be distantly related to coexisting species. Here, we document a 19-y decline of phylogenetic diversity in a grassland community as moisture became less abundant and predictable at a critical time of the year. This decline was strongest in native forbs, particularly those with high specific leaf area, a trait indicating drought sensitivity. This decline occurred at the small spatial scale where species interact, but the larger regional community has so far been buffered against loss of phylogenetic diversity by its high levels of physical and biotic heterogeneity.

Trait-based signatures of cloud base height in a tropical cloud forest.

PREMISE: Clouds have profound consequences for ecosystem structure and function. Yet, the direct monitoring of clouds and their effects on biota is challenging especially in remote and topographically complex tropical cloud forests. We argue that known relationships between climate and the taxonomic and functional composition of plant communities may provide a fingerprint of cloud base height, thus providing a rapid and cost-effective assessment in remote tropical cloud forests. METHODS: To detect cloud base height, we compared species turnover and functional trait values among herbaceous and woody plant communities in an ecosystem dominated by cloud formation. We measured soil and air temperature, soil nutrient concentrations, and extracellular enzyme activity. We hypothesized that woody and herbaceous plants would provide signatures of cloud base height, as evidenced by abrupt shifts in both taxonomic composition and plant function. RESULTS: We demonstrated abrupt changes in taxonomic composition and the community- weighted mean of a key functional trait, specific leaf area, across elevation for both woody and herbaceous species, consistent with our predictions. However, abrupt taxonomic and functional changes occurred 100 m higher in elevation for herbaceous plants compared to woody ones. Soil temperature abruptly decreased where herbaceous taxonomic and functional turnover was high. Other environmental variables including soil biogeochemistry did not explain the abrupt change observed for woody plant communities. CONCLUSIONS: We provide evidence that a trait-based approach can be used to estimate cloud base height. We outline how rises in cloud base height and differential environmental requirements between growth forms can be distinguished using this approach.

Seed banks of native forbs, but not exotic grasses, increase during extreme drought.

Extreme droughts such as the one that affected California in 2012-2015 have been linked to severe ecological consequences in perennial-dominated communities such as forests. In annual communities, drought impacts are difficult to assess because many species persist through facultative multiyear seed dormancy, which leads to the development of seed banks. Impacts of extreme drought on the abundance and composition of the seed banks of whole communities are little known. In 80 heterogeneous grassland plots where cover is dominated by ~15 species of exotic annual grasses and diversity is dominated by ~70 species of native annual forbs, we grew out seeds from soil cores collected early in the California drought (2012) and later in the multiyear drought (2014), and analyzed drought-associated changes in the seed bank. Over the course of the study we identified more than 22,000 seedlings to species. We found that seeds of exotic annual grasses declined sharply in abundance during the drought while seeds of native annual forbs increased, a pattern that resembled but was even stronger than the changes in aboveground cover of these groups. Consistent with the expectation that low specific leaf area (SLA) is an indicator of drought tolerance, we found that the community-weighted mean SLA of annual forbs declined both in the seed bank and in the aboveground community, as low-SLA forbs increased disproportionately. In this system, seed dormancy reinforces the indirect benefits of extreme drought to the native forb community.

Climate-driven diversity change in annual grasslands: Drought plus deluge does not equal normal.

Climate forecasts agree that increased variability and extremes will tend to reduce the availability of water in many terrestrial ecosystems. Increasingly severe droughts may be exacerbated both by warmer temperatures and by the relative unavailability of water that arrives in more sporadic and intense rainfall events. Using long-term data and an experimental water manipulation, we examined the resilience of a heterogeneous annual grassland community to a prolonged series of dry winters that led to a decline in plant species richness (2000-2014), followed by a near-record wet winter (2016-2017), a climatic sequence that broadly resembles the predicted future in its high variability. In our 80, 5-m2 observational plots, species richness did not recover in response to the wet winter, and the positive relationship of richness to annual winter rainfall thus showed a significant weakening trend over the 18-year time period. In experiments on 100, 1-m2 plots, wintertime water supplementation increased and drought shelters decreased the seedling survival and final individual biomass of native annual forbs, the main functional group contributing to the observed long-term decline in richness. Water supplementation also increased the total cover of native annual forbs, but only increased richness within nested subplots to which seeds were also added. We conclude that prolonged dry winters, by increasing seedling mortality and reducing growth of native forbs, may have diminished the seedbank and thus the recovery potential of diversity in this community. However, the wet winter and the watering treatment did cause recovery of the community mean values of a key functional trait (specific leaf area, an indicator of drought intolerance), suggesting that some aggregate community properties may be stabilized by functional redundancy among species.

Towards an eco-evolutionary understanding of endemism hotspots and refugia.

Background: Refugia are island-like habitats that are linked to long-term environmental stability and, as a result, high endemism. Conservation of refugia and endemism hotspots should be based on a deep ecological and evolutionary understanding of their functioning, which remains limited. Although functional traits can provide such insights, a corresponding, coherent framework is lacking. Proposed Framework: Plant communities in refugia and endemism hotspots should, due to long-term environmental stability, display unique functional characteristics linked to distinct phylogenetic patterns. Therefore, such communities should be characterized by a functional signature that exhibits: (1) distinct values and combinations of traits, (2) higher functional diversity and (3) a prevalence of similar traits belonging to more distantly related lineages inside, compared to outside, of endemism hotspots and refugia. While the limited functional trait data available from refugia and endemism hotspots do not allow these predictions to be tested rigorously, three potential applications of the functional signature in biogeography and conservation planning are highlighted. Firstly, it allows the functional characteristics of endemism hotspots and refugia to be identified. Secondly, the strength of the functional signature can be compared among these entities, and with the surrounding landscape, to provide an estimate of the capacity of endemism hotspots and refugia to buffer environmental changes. Finally, the pattern of the functional signature can reveal ecological and evolutionary processes driving community assembly and functioning, which can assist in predicting the effect of environmental changes (e.g. climate, land-use) on communities in endemism hotspots and refugia. Conclusion: The proposed functional signature concept allows the systematic integration of plant functional traits and phylogeny into the study of endemism hotspots and refugia, but more data on functional traits in these entities are urgently needed. Overcoming this limitation would facilitate rigorous testing of the proposed predictions for the functional signature, advancing the eco-evolutionary understanding of endemism hotspots and refugia.

Resource colimitation governs plant community responses to altered precipitation.

Ecological theory and evidence suggest that plant community biomass and composition may often be jointly controlled by climatic water availability and soil nutrient supply. To the extent that such colimitation operates, alterations in water availability caused by climatic change may have relatively little effect on plant communities on nutrient-poor soils. We tested this prediction with a 5-y rainfall and nutrient manipulation in a semiarid annual grassland system with highly heterogeneous soil nutrient supplies. On nutrient-poor soils, rainfall addition alone had little impact, but rainfall and nutrient addition synergized to cause large increases in biomass, declines in diversity, and near-complete species turnover. Plant species with resource-conservative functional traits (low specific leaf area, short stature) were replaced by species with resource-acquisitive functional traits (high specific leaf area, tall stature). On nutrient-rich soils, in contrast, rainfall addition alone caused substantial increases in biomass, whereas fertilization had little effect. Our results highlight that multiple resource limitation is a critical aspect when predicting the relative vulnerability of natural communities to climatically induced compositional change and diversity loss.

Climate-driven diversity loss in a grassland community.

Local ecological communities represent the scale at which species coexist and share resources, and at which diversity has been experimentally shown to underlie stability, productivity, invasion resistance, and other desirable community properties. Globally, community diversity shows a mixture of increases and decreases over recent decades, and these changes have relatively seldom been linked to climatic trends. In a heterogeneous California grassland, we documented declining plant diversity from 2000 to 2014 at both the local community (5 m(2)) and landscape (27 km(2)) scales, across multiple functional groups and soil environments. Communities became particularly poorer in native annual forbs, which are present as small seedlings in midwinter; within native annual forbs, community composition changed toward lower representation of species with a trait indicating drought intolerance (high specific leaf area). Time series models linked diversity decline to the significant decrease in midwinter precipitation. Livestock grazing history, fire, succession, N deposition, and increases in exotic species could be ruled out as contributing causes. This finding is among the first demonstrations to our knowledge of climate-driven directional loss of species diversity in ecological communities in a natural (nonexperimental) setting. Such diversity losses, which may also foreshadow larger-scale extinctions, may be especially likely in semiarid regions that are undergoing climatic trends toward higher aridity and lower productivity.

Endemism hotspots are linked to stable climatic refugia.

BACKGROUND: Centres of endemism have received much attention from evolutionists, biogeographers, ecologists and conservationists. Climatic stability is often cited as a major reason for the occurrences of these geographic concentrations of species which are not found anywhere else. The proposed linkage between endemism and climatic stability raises unanswered questions about the persistence of biodiversity during the present era of rapidly changing climate. KEY QUESTIONS: The current status of evidence linking geographic centres of endemism to climatic stability over evolutionary time was examined. The following questions were asked. Do macroecological analyses support such an endemism-stability linkage? Do comparative studies find that endemic species display traits reflecting evolution in stable climates? Will centres of endemism in microrefugia or macrorefugia remain relatively stable and capable of supporting high biological diversity into the future? What are the implications of the endemism-stability linkage for conservation? CONCLUSIONS: Recent work using the concept of climate change velocity supports the classic idea that centres of endemism occur where past climatic fluctuations have been mild and where mountainous topography or favourable ocean currents contribute to creating refugia. Our knowledge of trait differences between narrow endemics and more widely distributed species remains highly incomplete. Current knowledge suggests that centres of endemism will remain relatively climatically buffered in the future, with the important caveat that absolute levels of climatic change and species losses in these regions may still be large.

Effect of cell permeability and dehydrogenase expression on octane activation by CYP153A6-based whole cell Escherichia coli catalysts.

BACKGROUND: The regeneration of cofactors and the supply of alkane substrate are key considerations for the biocatalytic activation of hydrocarbons by cytochrome P450s. This study focused on the biotransformation of n-octane to 1-octanol using resting Escherichia coli cells expressing the CYP153A6 operon, which includes the electron transport proteins ferredoxin and ferredoxin reductase. Glycerol dehydrogenase was co-expressed with the CYP153A6 operon to investigate the effects of boosting cofactor regeneration. In order to overcome the alkane supply bottleneck, various chemical and physical approaches to membrane permeabilisation were tested in strains with or without additional dehydrogenase expression. RESULTS: Dehydrogenase co-expression in whole cells did not improve product formation and reduced the stability of the system at high cell densities. Chemical permeabilisation resulted in initial hydroxylation rates that were up to two times higher than the whole cell system, but severely impacted biocatalyst stability. Mechanical cell breakage led to improved enzyme stability, but additional dehydrogenase expression was necessary to improve product formation. The best-performing system (in terms of final titres) consisted of mechanically ruptured cells expressing additional dehydrogenase. This system had an initial activity of 1.67 ± 0.12 U/gDCW (32% improvement on whole cells) and attained a product concentration of 34.8 ± 1.6 mM after 24 h (22% improvement on whole cells). Furthermore, the system was able to maintain activity when biotransformation was extended to 72 h, resulting in a final product titre of 60.9 ± 1.1 mM. CONCLUSIONS: This study suggests that CYP153A6 in whole cells is limited by coupling efficiencies rather than cofactor supply. However, the most significant limitation in the current system is hydrocarbon transport, with substrate import being the main determinant of hydroxylation rates, and product export playing a key role in system stability.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN-), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN- loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN-. A second reactor was fed ammonium sulfate to mimic breakdown products of SCN-. Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN- reactor, Thiobacillus strains capable of SCN- degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN- reactor expressed proteins involved in SCN- degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.

Integrin α6ß4 Promotes Autocrine Epidermal Growth Factor Receptor (EGFR) Signaling to Stimulate Migration and Invasion toward Hepatocyte Growth Factor (HGF).

Integrin α6ß4 is up-regulated in pancreatic adenocarcinomas where it contributes to carcinoma cell invasion by altering the transcriptome. In this study, we found that integrin α6ß4 up-regulates several genes in the epidermal growth factor receptor (EGFR) pathway, including amphiregulin (AREG), epiregulin (EREG), and ectodomain cleavage protease MMP1, which is mediated by promoter demethylation and NFAT5. The correlation of these genes with integrin α6ß4 was confirmed in The Cancer Genome Atlas Pancreatic Cancer Database. Based on previous observations that integrin α6ß4 cooperates with c-Met in pancreatic cancers, we examined the impact of EGFR signaling on hepatocyte growth factor (HGF)-stimulated migration and invasion. We found that AREG and EREG were required for autocrine EGFR signaling, as knocking down either ligand inhibited HGF-mediated migration and invasion. We further determined that HGF induced secretion of AREG, which is dependent on integrin-growth factor signaling pathways, including MAPK, PI3K, and PKC. Moreover, matrix metalloproteinase activity and integrin α6ß4 signaling were required for AREG secretion. Blocking EGFR signaling with EGFR-specific antibodies or an EGFR tyrosine kinase inhibitor hindered HGF-stimulated pancreatic carcinoma cell chemotaxis and invasive growth in three-dimensional culture. Finally, we found that EGFR was phosphorylated in response to HGF stimulation that is dependent on EGFR kinase activity; however, c-Met phosphorylation in response to HGF was unaffected by EGFR signaling. Taken together, these data illustrate that integrin α6ß4 stimulates invasion by promoting autocrine EGFR signaling through transcriptional up-regulation of key EGFR family members and by facilitating HGF-stimulated EGFR ligand secretion. These signaling events, in turn, promote pancreatic carcinoma migration and invasion.

Shading and litter mediate the effects of soil fertility on the performance of an understorey herb.

BACKGROUND AND AIMS: Soil fertility and topographic microclimate are common determinants of plant species distributions. However, biotic conditions also vary along these abiotic gradients, and may mediate their effects on plants. In this study, we investigated whether soils and topographic microclimate acted directly on the performance of a focal understorey plant, or indirectly via changing biotic conditions. METHODS: We examined direct and indirect relationships between abiotic variables (soil fertility and topographic microclimate) and biotic factors (overstorey and understorey cover, litter depth and mycorrhizal colonization) and the occurrence, density and flowering of a common understorey herb, Trientalis latifolia, in the Klamath-Siskiyou Mountains, Oregon, USA. RESULTS: We found that the positive effects of soil fertility on Trientalis occurrence were mediated by greater overstorey shading and deeper litter. However, we did not find any effects of topographic microclimate on Trientalis distribution that were mediated by the biotic variables we measured. The predictive success of Trientalis species distribution models with soils and topographic microclimate increased by 12 % with the addition of the biotic variables. CONCLUSIONS: Our results reinforce the idea that species distributions are the outcome of interrelated abiotic gradients and biotic interactions, and suggest that biotic conditions, such as overstorey density, should be included in species distribution models if data are available.

Species diversity is dynamic and unbounded at local and continental scales.

We argue that biotas at scales from local communities to entire continents are nearly always open to new species and that their diversities are far from any ecological limits. We show that the fossil, phylogenetic, and morphological evidence that has been used to suggest that ecological processes set limits to diversity in evolutionary time is weak and inconsistent. At the same time, ecological evidence from biological invasions, experiments, and diversity analyses strongly supports the openness of communities to new species. We urge evolutionary biologists to recognize that ecology has largely moved beyond simple notions of equilibrium at a carrying capacity and toward a richer view of communities as highly dynamic in space and time.