Responses Of Taxa Research Articles

Enhanced carbon use efficiency and warming resistance of soil microorganisms under organic amendment

The frequency and intensity of extreme weather events, including rapid temperature fluctuations, are increasing because of climate change. Long-term fertilization practices have been observed to alter microbial physiology and community structure, thereby affecting soil carbon sequestration. However, the effects of warming on the carbon sequestration potential of soil microbes adapted to long-term fertilization remain poorly understood. In this study, we utilized 18O isotope labeling to assess microbial carbon use efficiency (CUE) and employed stable isotope probing (SIP) with 18O-H2O to identify growing taxa in response to temperature changes (5–35 °C). Organic amendment with manure or straw residue significantly increased microbial CUE by 86–181 % compared to unfertilized soils. The microorganisms inhabiting organic amended soils displayed greater resistance of microbial CUE to high temperatures (25–35 °C) compared to those inhabiting soils fertilized only with minerals. Microbial growth patterns determined by the classification of taxa into incorporators or non-incorporators based on 18O incorporation into DNA exhibited limited phylogenetic conservation in response to temperature changes. Microbial clusters were identified by grouping taxa with similar growth patterns across different temperatures. Organic amendments enriched microbial clusters associated with increased CUE, whereas clusters in unfertilized or mineral-only fertilized soils were linked to decreased CUE. Specifically, shifts in the composition of growing bacteria were correlated with enhanced microbial CUE, whereas modifications in the composition of growing fungi were associated with diminished CUE. Notably, the responses of microbial CUE to temperature fluctuations were primarily driven by changes in the bacterial composition. Overall, our findings demonstrate that organic amendments enhance soil microbial CUE and promote the enrichment of specific microbial clusters that are better equipped to cope with temperature changes. This study establishes a theoretical foundation for manipulating soil microbes to enhance carbon sequestration under global climate scenarios.

Modeling individual growth reveals decreasing gray whale body length and correlations with ocean climate indices at multiple scales

AbstractChanges in body size have been documented across taxa in response to human activities and climate change. Body size influences many aspects of an individual's physiology, behavior, and ecology, ultimately affecting life history performance and resilience to stressors. In this study, we developed an analytical approach to model individual growth patterns using aerial imagery collected via drones, which can be used to investigate shifts in body size in a population and the associated drivers. We applied the method to a large morphological dataset of gray whales (Eschrichtius robustus) using a distinct foraging ground along the NE Pacific coast, and found that the asymptotic length of these whales has declined since around the year 2000 at an average rate of 0.05–0.12 m/y. The decline has been stronger in females, which are estimated to be now comparable in size to males, minimizing sexual dimorphism. We show that the decline in asymptotic length is correlated with two oceanographic metrics acting as proxies of habitat quality at different scales: the mean Pacific Decadal Oscillation index, and the mean ratio between upwelling intensity in a season and the number of relaxation events. These results suggest that the decline in gray whale body size may represent a plastic response to changing environmental conditions. Decreasing body size could have cascading effects on the population's demography, ability to adjust to environmental changes, and ecological influence on the structure of their community. This finding adds to the mounting evidence that body size is shrinking in several marine populations in association with climate change and other anthropogenic stressors. Our modeling approach is broadly applicable across multiple systems where morphological data on megafauna are collected using drones.

Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.

Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.

Phytoplankton communities of the west coast of Florida – multiyear and seasonal responses to nutrient enrichment

Blooms of the harmful algae species Karenia brevis are frequent off the southwest coast of Florida despite having relatively slow growth rates. The regional frequency of these harmful algal blooms led to the examination of the dominant estuarine outflows for effects on both K. brevis and the phytoplankton community in general. There is comparatively little information on the growth rates of non-Karenia taxonomic groups other than diatoms. A seasonally based series (Fall, Winter, and Spring) of bioassay experiments were conducted to determine the nutrient response of the coastal phytoplankton community. Treatments included estuarine waters (Tampa Bay, Charlotte Harbor, and the Caloosahatchee River) applied in a 1:25 dilution added to coastal water to mimic the influence of estuarine water in a coastal environment. Other treatments were 5–15 μM additions of nitrogen (N), phosphorus (P), and silica (Si) species, amino acids, and N (urea) + P added to coastal water. Incubations were conducted under ambient conditions with shading for 48 h. Analyses of dissolved and particulate nutrients were coupled with HPLC analysis of characteristic photopigments and taxonomic assignments of biomass via CHEMTAX. The coastal phytoplankton community, dominated by diatoms, cyanophytes and prasinophytes, was significantly different both by bioassay and by season, indicating little seasonal fidelity in composition. Specific growth rates of chlorophyll a indicated no significant difference between any controls, any estuarine treatment, P, or Si treatments. Conditions were uniformly N-limited with the highest growth rates in diatom biomass. Despite differing initial communities, however, there were seasonally reproducible changes in community due to the persistent growth or decline of the various taxa, including haptophytes, cyanophytes, and cryptophytes. For the one bioassay in which K. brevis was present, the slow growth of K. brevis relative to diatoms in a mixed community was evident, indicating that identifying the seasonally based behavior of other taxa in response to nutrients is critical for the simulation of phytoplankton competition and the successful prediction of the region's harmful algal blooms.

Coordination of Root Traits and Rhizosphere Microbial Community in Tea (Camellia sinensis L.) Plants under Drought and Rehydration

Soil drought and rehydration have an immense impact on plant physiology and productivity, whereas the response of plant–microbe interactions to varied water availability remains largely elusive. In this study, two tea (Camellia sinensis L.) cultivars, Longjing43 and Yingshuang, were subjected to drought followed by rehydration. Soil drought significantly induced the elongation of taproots in the Yingshuang cultivar after two weeks of drought. Moreover, the four-week drought significantly reduced the root dry mass and root nitrogen, phosphorus, and potassium concentrations in both tea cultivars. Two-week rehydration recovered the root potassium concentration in the two tea cultivars, revealing the rapid response of root potassium levels to water conditions. Drought and rehydration also resulted in shifts in rhizosphere microbial diversity. A four-week drought reduced microbial alpha diversity in Longjing43 but not in the Yingshuang cultivar, and rehydration was effective in restoring alpha diversity in Longjing43. The rhizosphere microbial community tended to recover to the initial stages after rehydration in Longjing43 but not in the other cultivar. In addition, 18 microbial genera were identified as the featured microbial taxa in response to varied water availability, and a rare genus Ignavibacterium was significantly increased in the Longjing43 cultivar by rehydration after a four-week drought. Furthermore, root nitrogen, phosphorus, potassium levels, and dry mass were positively correlated with the microbial alpha diversity, while the taproot length was negatively correlated, suggesting the crucial role of plant–microbe interactions in response to drought and rehydration. Moreover, the root phosphorus concentration and taproot length also had significant effects on microbial beta diversity, further confirming their effects on the community structure of the rhizosphere microbiome. Overall, this study provides insights into the effects of drought on plant–microbe interactions in the rhizosphere of tea plants. These findings are important for harnessing the roles of the tea rhizosphere microbiome under drought.

Footprints of predatory lady beetles stimulate increased dispersal of aphid prey, but do not alter feeding behavior or spread of a non-persistently transmitted plant virus

Predators impact prey directly, through consumption, and indirectly, through non-consumptive effects that modify prey physiology and behavior in ways that affect survival and reproduction. Non-consumptive effects (NCEs) are well documented across prey taxa in response to different predator cues. However, for most prey species, both the mechanisms underlying NCEs and the impacts of NCEs on broader ecological processes are poorly understood. We addressed these knowledge gaps for an aphid prey species (Myzus persicae) by studying dispersal, in-leaf feeding behavior, and plant virus transmission in response to chemical cues deposited by a walking predator (Hippodamia convergens), a non-predator, non-competitor (Drosophila melanogaster), and an artificial feeding deterrent (2% mineral oil). We used this approach to better understand the specificity of M. persicae responses to chemical footprints of threatening and non-threatening organisms, as well as the magnitude of behavioral responses relative to a known deterrent. We found that chemical footprints deposited by H. convergens stimulated M. persicae to disperse from a suitable host (Brassica napus) at a rate equivalent to the 2% mineral oil positive control, while footprints of D. melanogaster did not modify M. persicae dispersal. Through electrical penetration graphing (EPG) recordings, we found that mineral oil stimulated aphids to make more probes, but footprint treatments did not significantly modify feeding behavior. In mesocosm-based virus transmission assays, H. convergens footprints and 2% mineral oil also stimulated increased dispersal, but this did not translate into increased transmission of turnip mosaic virus. We identified components of H. convergens and D. melanogaster footprints using gas chromatography and mass spectrometry and found that H. convergens footprints are chemically similar to footprints of related Coccinellidae, but distinct from D. melanogaster footprints. Our results provide evidence of specificity in M. persicae responses to predator footprints, which may help this prey species avoid costly dispersal behavior in response to cues from non-predators. We also provide ecological context by demonstrating that increased dispersal in response to predator cues does not always lead to increased virus transmission, as previously assumed, particularly when in-leaf feeding behaviors underlying virus acquisition do not change in response to predator cues.

Disturbance intensification is altering the trait composition of Caribbean reefs, locking them into a low functioning state

Anthropogenic climate change is intensifying natural disturbance regimes, which negatively affects some species, while benefiting others. This could alter the trait composition of ecological communities and influence resilience to disturbance. We investigated how the frequency and intensification of the regional storm regime (and likely other disturbances) is altering coral species composition and in turn resistance and recovery. We developed regional databases of coral cover and composition (3144 reef locations from 1970 to 2017) and of the path and strength of cyclonic storms in the region (including 10,058 unique storm-reef intersections). We found that total living coral cover declined steadily through 2017 (the median annual loss rate was ~ 0.25% per year). Our results also indicate that despite the observed increase in the intensity of Atlantic cyclonic storms, their effect on coral cover has decreased markedly. This could be due in part to selection for disturbance-resistant taxa in response to the intensifying disturbance regime. We found that storms accelerated the loss of threatened acroporid corals but had no measurable effect on the cover of more resilient “weedy” corals, thereby increasing their relative cover. Although resistance to disturbance has increased, recovery rates have slowed due to the dominance of small, slow-growing species. This feedback loop is locking coral communities into a low-functioning state dominated by weedy species with limited ecological or societal value.

Response of soil microbial community structure, carbon and nitrogen cycling to drying and rewetting

Global change scenarios predict that precipitation regimes will become more variable in many parts of the world, extending drought periods and increasing rainfall intensity. Under these conditions, soil microbial community composition will likely change in ways that have implications for microbially-mediated nutrient cycling. Understanding these responses is key to predicting consequential changes in ecosystem functions. A 30 day incubation experiment was used to investigate the response of microbial community structure to three different soil moisture treatments, namely, constantly moist (CM), constantly dry (CD), and drying-rewetting (DRW), in soils of three different land condition types (Remnant, Restored, and Old-field) from Para Woodlands Nature Reserve, South Australia. Soil respiration and inorganic N transformations were approximately the same across soils, despite fundamental differences in physicochemical properties, vegetation communities, and land-use history. Soil microbial community structure changed in response to the different soil moisture treatments; responses of taxa was divergent among soils. These results demonstrate that changes to soil moisture regimes under climate projections will almost certainly have consequences for soil microbial communities and C and N dynamics. The results highlight the need for further research to understand the mechanisms driving divergent responses to soil moisture, particularly in areas of different land-use types.

Response of soil microbial Communities, inorganic and organic soil carbon pools in arid saline soils to alternative land use practices

Soil organic and inorganic carbon (SOC & SIC) and microbial community structure are key indicators of soil quality and productivity in arid-saline soils. Salinity stress and diminishing availability of freshwater (FW) for irrigation are major constraints for productivity and improving soil quality indicators. Using treated wastewater (TW) and implementing climate-smart cropping systems are promising alternatives to replace freshwater usage in intensive cropping systems, however, impacts on the microbial community and net-carbon sequestration potential are not clearly understood. This field study was conducted in an arid saline-soil to investigate soil microbial community structure and soil carbon contents under a combination of treatments comparing bioenergy sorghum (So) and switchgrass (Sg), two irrigation water sources (FW & TW), and gypsum amendment (GA), to a native-soil control. After three years of implementing these treatments, soil samples were collected and analyzed for total carbon (TC), SOC, SIC, microbial biomass-carbon (MBC) and microbial community structure. Results showed that TW increased microbial diversity and shifted the community structure towards copiotroph-dominated prokaryotes. Several predominant and responsive taxa were associated with divergent trends of SOC, SIC and salinity parameters. Both SOC and SIC pools were sensitive to treatments and demonstrated divergent trends, as contents of TC and SOC were higher in TW-treatments, but of SIC were significantly lower in several So_TW treatments. Treatment TW_So_GA assembled a distinctive microbial community structure, accumulated the highest content of SOC (7.66 g kg−1) but recorded the lowest content of SIC (6.63 g kg−1). The lowest content of SOC was observed in native soil (4.58 g kg−1) but contained the highest SIC (8.15 g kg−1). The study results revealed the agronomic systems with higher potential for increasing TC and SOC content in arid-saline soils. Surface soil SIC was responsive to agronomic management, and several treatments produced disparate impacts on SOC and SIC stocks, which warrant for considering TC as the key indicator for assessing carbon sequestration in arid lands.

Cuttlefish color change as an emerging proxy for ecotoxicology.

Lately, behavioral ecotoxicology has flourished because of increasing standardization of analyses of endpoints like movement. However, research tends to focus on a few model species, which limits possibilities of extrapolating and predicting toxicological effects and adverse outcomes at the population and ecosystem level. In this regard, it is recommended to assess critical species-specific behavioral responses in taxa playing key roles in trophic food webs, such as cephalopods. These latter, known as masters of camouflage, display rapid physiological color changes to conceal themselves and adapt to their surrounding environments. The efficiency of this process depends on visual abilities and acuity, information processing, and control of chromatophores dynamics through nervous and hormonal regulation with which many contaminants can interfere. Therefore, the quantitative measurement of color change in cephalopod species could be developed as a powerful endpoint for toxicological risk assessment. Based on a wide body of research having assessed the effect of various environmental stressors (pharmaceutical residues, metals, carbon dioxide, anti-fouling agents) on the camouflage abilities of juvenile common cuttlefish, we discuss the relevance of this species as a toxicological model and address the challenge of color change quantification and standardization through a comparative review of the available measurement techniques.

Long-term fungus–plant covariation from multi-site sedimentary ancient DNA metabarcoding

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the co-occurrence of plants and fungi across selected sites in Siberia.We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. We obtained 706 unique fungal operational taxonomic units (OTUs) and 243 taxa for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedbacks between fungus composition and plant diversity changes which will affect forest advance, species diversity, and ecosystem stability in arctic regions.

Different roles of core and noncore bacterial taxa in maintaining soil multinutrient cycling and microbial network stability in arid fertigation agroecosystems

Abstract Microbes play an essential role in soil biogeochemical processes and maintenance of soil nutrients, but not all microbial taxa contribute equally, and their functions in soil nutrient cycling and microbial network stability are unclear in arid fertigation agricultural ecosystems. In this study, a 4‐year field experiment was conducted in an irrigation district in China using three levels of irrigation [high (400 mm), medium (300 mm) and low (200 mm)] and two levels of fertilization [high (600 kg/ha P2O5 + 300 kg/ha urea) and low (300 kg/ha P2O5 + 150 kg/ha urea)] to reveal the ecological roles of core and noncore taxa in maintaining soil nutrient cycling and their associations with microbial network stability. Our results showed that combining medium irrigation with low fertilization resulted in higher levels of soil organic C, inorganic N, available P, multinutrient cycling and noncore bacterial diversity compared with the other treatments. Soils supporting a higher diversity of noncore bacterial taxa had a high soil multinutrient cycling index, while soils harbouring highly diverse core taxa exhibited a more stable bacterial network. The soil multinutrient cycling index was also significantly positively related to the subnetwork modularity of noncore taxa. Moreover, noncore taxa could serve as diverse pools that turn into core taxa in response to changes in the external environment. Acinetobacter, Flavobacterium, Gemmatimonas and Salinimicrobium, which belong to the noncore taxa, were involved in soil C and N cycling in the arid agricultural ecosystem. Synthesis and applications. Our results suggest that soil microbiota contribute differently to ecosystem functions. Changes in soil nutrient cycling were more closely related to variations in noncore taxa, while bacterial network stability was more associated with core taxa. Our study emphasized the role of noncore microbiota, which has been neglected in previous studies. Furthermore, our findings suggested that combining medium irrigation with low fertilization is effective for enhancing soil nutrients and bacterial diversity, providing guidance for managing arid agricultural ecosystems.

Partitioning of beta-diversity reveals distinct assembly mechanisms of plant and soil microbial communities in response to nitrogen enrichment.

Nitrogen (N) deposition poses a serious threat to terrestrial biodiversity and alters plant and soil microbial community composition. Species turnover and nestedness reflect the underlying mechanisms of variations in community composition. However, it remains unclear how species turnover and nestedness contribute to different responses of taxonomic groups (plants and soil microbes) to N enrichment. Here, based on a 13‐year consecutive multi‐level N addition experiment in a semiarid steppe, we partitioned community β‐diversity into species turnover and nestedness components and explored how and why plant and microbial communities reorganize via these two processes following N enrichment. We found that plant, soil bacterial, and fungal β‐diversity increased, but their two components showed different patterns with increasing N input. Plant β‐diversity was mainly driven by species turnover under lower N input but by nestedness under higher N input, which may be due to a reduction in forb species, with low tolerance to soil Mn2+, with increasing N input. However, turnover was the main contributor to differences in soil bacterial and fungal communities with increasing N input, indicating the phenomenon of microbial taxa replacement. The turnover of bacteria increased greatly whereas that of fungi remained within a narrow range with increasing N input. We further found that the increased soil Mn2+ concentration was the best predictor for increasing nestedness of plant communities under higher N input, whereas increasing N availability and acidification together contributed to the turnover of bacterial communities. However, environmental factors could explain neither fungal turnover nor nestedness. Our findings reflect two different pathways of community changes in plants, soil bacteria, and fungi, as well as their distinct community assembly in response to N enrichment. Disentangling the turnover and nestedness of plant and microbial β‐diversity would have important implications for understanding plant–soil microbe interactions and seeking conservation strategies for maintaining regional diversity.

Match/Mismatch Between Phytoplankton and Crustacean Zooplankton Phenology in the Strait of Georgia, Canada

The Strait of Georgia, Canada, is an important region for numerous commercially and culturally important species (e.g., herring, salmon, and orcas), yet little is known about the links between lower trophic level (e.g. phytoplankton and zooplankton) phenology due to historical sampling gaps. Here, we present fourteen years (2003-2016) of data linking interannual variability in phytoplankton and zooplankton phenology in the Central Strait of Georgia, BC. Satellite-derived chlorophyll a (Chl a) data were used to calculate spring bloom dynamics (bloom initiation, bloom intensity, and bloom magnitude). Average spring bloom initiation occurred during the last week of March in the Central Strait of Georgia. Bloom initiation occurred in mid-to-late February/early March during “early” Chl a bloom years (2004, 2005, and 2015) whereas initiation did not occur until the end of April during “late” bloom years (2007, 2008). Spring Chl a bloom initiation was significantly correlated with the North Pacific Gyre Oscillation (NPGO; r = 0.75, p < 0.01) and spring sea surface temperature (SST; r = -0.70, p < 0.01); spring blooms occurred earlier during warm years. When all environmental variables were considered together, NPGO best explained variations in spring bloom initiation (Adj R2 = 0.53, p < 0.01) and bloom magnitude (Adj R2 = 0.57, p < 0.01), whereas stratification best explained variations in bloom intensity (Adj R2 = 0.38, p < 0.05). Early Chl a blooms were associated with high crustacean abundance (maximum of > 1000 ind m-3) but low biomass (37.5 mg m-3). Independent of the Chl a data, hierarchical cluster analysis revealed similar groupings of years for crustacean abundance data. Most notably, community composition in cluster Group 2 (2004, 2005, and 2015; early Chl a bloom years), was comprised of a higher proportion of small crustaceans (e.g. non-calanoid copepods) compared to the other cluster groups. To our knowledge, this study provides the first evidence linking early spring Chl a bloom timing to a shift in the crustacean community towards smaller taxa in response to multiple warm events in the Strait of Georgia. Our results show that early Chl a blooms may potentially result in a mismatch between phytoplankton and large energy-rich crustacean zooplankton, with lower abundances of the latter. In contrast, average Chl a bloom years were optimal for large-bodied euphausiids, whereas late Chl a blooms were a match for some crustaceans (e.g., medium calanoid copepods), but not others (e.g., large calanoid copepods and amphipods). We hypothesize that early bloom years may result in poorer feeding conditions for juvenile salmon and other predators in the region.

Toward the use of protists as bioindicators of multiple stresses in agricultural soils: A case study in vineyard ecosystems

Management of agricultural soil quality requires fast and cost-efficient methods to identify multiple stressors that can affect soil organisms and associated ecological processes. Here, we propose to use soil protists which have a great yet poorly explored potential for bioindication. They are ubiquitous, highly diverse, and respond to various stresses to agricultural soils caused by frequent management or environmental changes.We test an approach that combines metabarcoding data and machine learning algorithms to identify potential stressors of soil protist community composition and diversity. We measured 17 key variables that reflect various potential stresses on soil protists across 132 plots in 28 Swiss vineyards over 2 years. We identified the taxa showing strong responses to the selected soil variables (potential bioindicator taxa) and tested for their predictive power.Changes in protist taxa occurrence and, to a lesser extent, diversity metrics exhibited great predictive power for the considered soil variables. Soil copper concentration, moisture, pH, and basal respiration were the best predicted soil variables, suggesting that protists are particularly responsive to stresses caused by these variables. The most responsive taxa were found within the clades Rhizaria and Alveolata. Our results also reveal that a majority of the potential bioindicators identified in this study can be used across years, in different regions and across different grape varieties.Altogether, soil protist metabarcoding data combined with machine learning can help identifying specific abiotic stresses on microbial communities caused by agricultural management. Such an approach provides complementary information to existing soil monitoring tools that can help manage the impact of agricultural practices on soil biodiversity and quality.

Paleoceanographic inferences from benthic foraminifera across the early Aptian Ocean Anoxic Event 1a in the western Tethys

The paleoenvironmental impact of the early Aptian Ocean Anoxic Event 1a (OAE 1a, ca. 121 Ma) has been investigated in detail in the Cismon Core (Lombardy Basin, western Tethys) by using different geochemical and micropaleontological proxies. We provide the first high-resolution data of benthic foraminiferal assemblages through the upper Barremian - lower upper Aptian stratigraphic interval. Benthic foraminifera data are integrated with calcareous nannofossil and planktonic foraminifera records to create a comprehensive characterization of bottom and surface waters across OAE 1a. Benthic foraminiferal communities are indicative of a marked change in bottom-waters around the “nannoconid decline” (latest Barremian) due to increased flux of organic matter to the seafloor and intermittent dysoxic conditions probably promoted by pulses of higher productivity during the initial Greater Ontong Java Event (GOJE). Benthic foraminifera experienced a marked crisis in abundance (“benthic foraminiferal crisis” BFC) ca. 35 kyr before the OAE 1a, in correspondence with the “nannoconid crisis” and the onset of the most intense GOJE phase. The literature survey shows that the BFC is commonly recorded before the OAE 1a onset in several stratigraphic sections worldwide, and therefore, it is here proposed as a global event. At Cismon, deep-water anoxia was reached at the OAE 1a onset and lasted for ca. 300 kyr, promoted by higher productivity and eventually enhanced water stratification during the super-greenhouse climate. The continuation of OAE 1a was marked by a benthic foraminiferal repopulation event, probably resulting from the influx of relatively cooler and oxygenated waters. In turn, the OAE 1a was marked by intermittent anoxic to dysoxic conditions, likely in response to primary productivity sustained by N-fixing bacteria. The distribution and abundance of benthic foraminifera documented in other sections across the Selli Level equivalent show different features that point to local factors such as paleodepth and increased runoff. The post-OAE 1a was characterized by dysoxic conditions coupled with moderate organic matter flux to the seafloor. At the Cismon site and worldwide, the termination of OAE 1a coincided with the return of relatively more abundant benthic taxa in response to the restoration of favorable conditions allowing the development of diversified benthic foraminiferal communities.

Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items.

Food supply is one of the major drivers of animal behavior, and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi-level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here, we present a detailed year-round, multi-level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 seasons (total 120 days observations). For each individual, we found significant variation in the microbiome between all 4 seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds-sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome, and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species-level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds.

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.

Microbial Composition and Co-occurrence Patterns in the Gut Microbial Community of Normal and Obese Mice in Response to Astaxanthin.

The changes and interaction of gut microbiota, which respond to dietary supplements, play critical roles on improving human health. The modulating effect of astaxanthin on gut microbiota has been reported. However, little is known about the co-occurrence patterns among microbial taxa in response to astaxanthin. In this study, the gut microbial composition, co-occurrence patterns, and microbial correlations with physiological parameters in astaxanthin-fed normal and obese mice were studied. Astaxanthin altered the microbial composition and co-occurrence patterns in normal and obese mice. Furthermore, astaxanthin gave more profound impacts on microbiota in obesity when compared with normal mice. In group A (normal or obese mice supplemented with astaxanthin), the abundance of Acinetobacter was decreased, and Alistipes was increased by astaxanthin, which also occurred in the MA group (obese mice supplemented with astaxanthin). An operational taxonomic unit (OTU) (GreenGeneID# 4029632) assigned to the genus Bacteroides acted as a connector in the global network of A and MA groups. It may play critical roles in bridging intimate interactions between the host and other bacteria intervened by astaxanthin. Several modules correlated with physiological parameters were detected. For example, modules A12 and MA10 were significantly and negatively correlated with lipopolysaccharide (LPS) and fasting blood glucose (FBG) levels, respectively. A positive correlation was found between the node connectivity of the OTUs belonging to Clostridiaceae with LPS in obese mice, which indicated the role of Clostridiales as a potential pathological marker. Our findings provided a new interpretation of the role of astaxanthin in health and may contribute to further research on microbial community engineering.

Multiple thresholds and trajectories of microbial biodiversity predicted across browning gradients by neural networks and decision tree learning

Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that nonmonotonic relations dominate in nature. Here, we apply machine-learning algorithms to reveal the nonmonotonic association between microbial diversity and an anthropogenic-induced large-scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha-diversity) showed nonmonotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta-diversity) when applying standard methods assuming monotonic relations and up to 45% with machine-learning methods taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of nonmonotonic responses of individual bacterial sequence variants to browning. Furthermore, the nonmonotonic models provide the position of thresholds and predict alternative bacterial diversity trajectories in boreal freshwater as a result of ongoing climate and land-use changes, which in turn will affect entire ecosystem metabolism and likely greenhouse gas production.