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1. Evolutionary history and environmental variability structure contemporary tropical vertebrate communities

   https://doi.org/10.1111/geb.13829  

   Hsieh, Chia ; Gorczynski, Daniel ; Bitariho, Robert ; Espinosa, Santiago ; Johnson, Steig ; Lima, Marcela Guimarães Moreira ; Rovero, Francesco ; Salvador, Julia ; Santos, Fernanda ; Sheil, Douglas ; et al ( March 2024 , Global Ecology and Biogeography)

   Tropical regions harbour over half of the world's mammals and birds, but how their communities have assembled over evolutionary timescales remains unclear. To compare eco‐evolutionary assembly processes between tropical mammals and birds, we tested how hypotheses concerning niche conservatism, environmental stability, environmental heterogeneity and time‐for‐speciation relate to tropical vertebrate community phylogenetic and functional structure.

   Tropical rainforests worldwide.

   Present.

   Ground‐dwelling and ground‐visiting mammals and birds.

   We used in situ observations of species identified from systematic camera trap sampling as realized communities from 15 protected tropical rainforests in four tropical regions worldwide. We quantified standardized phylogenetic and functional structure for each community and estimated the multi‐trait phylogenetic signal (PS) in ecological strategies for the four regional species pools of mammals and birds. Using linear regression models, we test three non‐mutually exclusive hypotheses by comparing the relative importance of colonization time, palaeo‐environmental changes in temperature and land cover since 3.3 Mya, contemporary seasonality in temperature and productivity and environmental heterogeneity for predicting community phylogenetic and functional structure.

   Phylogenetic and functional structure showed non‐significant yet varying tendencies towards clustering or dispersion in all communities. Mammals had stronger multi‐trait PS in ecological strategies than birds (mean PS: mammal = 0.62, bird = 0.43). Distinct dominant processes were identified for mammal and bird communities. For mammals, colonization time and elevation range significantly predicted phylogenetic clustering and functional dispersion tendencies respectively. For birds, elevation range and contemporary temperature seasonality significantly predicted phylogenetic and functional clustering tendencies, respectively, while habitat diversity significantly predicted functional dispersion tendencies.

   Our results reveal different eco‐evolutionary assembly processes structuring contemporary tropical mammal and bird communities over evolutionary timescales that have shaped tropical diversity. Our study identified marked differences among taxonomic groups in the relative importance of historical colonization and sensitivity to environmental change.

    

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2. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

   https://doi.org/10.1186/s40168-022-01454-1  

   Kleiner, Manuel ; Kouris, Angela ; Violette, Marlene ; D’Angelo, Grace ; Liu, Yihua ; Korenek, Abigail ; Tolić, Nikola ; Sachsenberg, Timo ; McCalder, Janine ; Lipton, Mary S. ; et al ( February 2023 , Microbiome)

   Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput.

   Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software (https://sourceforge.net/projects/calis-p/). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using¹⁸O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were severalBacteroidesspecies known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics.

   We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

    

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3. Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality

   https://doi.org/10.1111/gcb.17088  

   Vompe, Alex D. ; Epstein, Hannah E. ; Speare, Kelly E. ; Schmeltzer, Emily R. ; Adam, Thomas C. ; Burkepile, Deron E. ; Sharpton, Thomas J. ; Vega Thurber, Rebecca ( December 2023 , Global Change Biology)

   Microbiomes are essential features of holobionts, providing their hosts with key metabolic and functional traits like resistance to environmental disturbances and diseases. In scleractinian corals, questions remain about the microbiome's role in resistance and resilience to factors contributing to the ongoing global coral decline and whether microbes serve as a form of holobiont ecological memory. To test if and how coral microbiomes affect host health outcomes during repeated disturbances, we conducted a large‐scale (32 exclosures, 200 colonies, and 3 coral species sampled) and long‐term (28 months, 2018–2020) manipulative experiment on the forereef of Mo'orea, French Polynesia. In 2019 and 2020, this reef experienced the two most severe marine heatwaves on record for the site. Our experiment and these events afforded us the opportunity to test microbiome dynamics and roles in the context of coral bleaching and mortality resulting from these successive and severe heatwaves. We report unique microbiome responses to repeated heatwaves inAcropora retusa,Porites lobata, andPocilloporaspp., which included: microbiome acclimatization inA. retusa, and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave inPocilloporaspp. Moreover, observed microbiome dynamics significantly correlated with coral species‐specific phenotypes. For example, bleaching and mortality inA. retusaboth significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, whileP. lobatacolonies had different microbiomes across mortality prevalence. Compositional microbiome changes, such as changes to proportions of differentially abundant putatively beneficial to putatively detrimental taxa to coral health outcomes during repeated heat stress, also correlated with host mortality, with higher proportions of detrimental taxa yielding higher mortality inA. retusa. This study reveals evidence for coral species‐specific microbial responses to repeated heatwaves and, importantly, suggests that host‐dependent microbiome dynamics may provide a form of holobiont ecological memory to repeated heat stress.

    

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4. Tropical pitcher plants (Nepenthes) act as ecological filters by altering properties of their fluid microenvironments

   https://doi.org/10.1038/s41598-020-61193-x  

   Gilbert, Kadeem J. ; Bittleston, Leonora S. ; Tong, Wenfei ; Pierce, Naomi E. ( March 2020 , Scientific Reports)

   Characteristics of host species can alter how other, interacting species assemble into communities by acting as ecological filters. Pitchers of tropical pitcher plants (Nepenthes) host diverse communities of aquatic arthropods and microbes in nature. This plant genus exhibits considerable interspecific diversity in morphology and physiology; for example, different species can actively control the pH of their pitcher fluids and some species produce viscoelastic fluids. Our study investigated the extent to whichNepenthesspecies differentially regulate pitcher fluid traits under common garden conditions, and the effects that these trait differences had on their associated communities. Sixteen species ofNepentheswere reared together in the controlled environment of a glasshouse using commonly-sourced pH 6.5 water. We analyzed their bacterial and eukaryotic communities using metabarcoding techniques, and found that different plant species differentially altered fluid pH, viscosity, and color, and these had strong effects on the community structure of their microbiota.Nepenthesspecies can therefore act as ecological filters, cultivating distinctive microbial communities despite similar external conditions, and blurring the conceptual line between biotic and abiotic filters.

    

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5. A direct comparison of ecological theories for predicting the relationship between plant traits and growth

   https://doi.org/10.1002/ecy.3986  

   Goud, Ellie M. ; Agrawal, Anurag A. ; Sparks, Jed P. ( March 2023 , Ecology)

   Despite long‐standing theory for classifying plant ecological strategies, limited data directly link organismal traits to whole‐plant growth rates (GRs). We compared trait‐growth relationships based on three prominent theories: growth analysis, Grime's competitive–stress tolerant–ruderal (CSR) triangle, and the leaf economics spectrum (LES). Under these schemes, growth is hypothesized to be predicted by traits related to relative biomass investment, leaf structure, or gas exchange, respectively. We also considered traits not included in these theories but that might provide potential alternative best predictors of growth. In phylogenetic analyses of 30 diverse milkweeds (Asclepiasspp.) and 21 morphological and physiological traits, GR (total biomass produced per day) varied 50‐fold and was best predicted by biomass allocation to leaves (as predicted by growth analysis) and the CSR traits of leaf size and leaf dry matter content. Total leaf area (LA) and plant height were also excellent predictors of whole‐plant GRs. Despite two LES traits correlating with growth (mass‐based leaf nitrogen and area‐based leaf phosphorus contents), these were in the opposite direction of that predicted by LES, such that higher N and P contents corresponded to slower growth. The remaining LES traits (e.g., leaf gas exchange) were not predictive of plant GRs. Overall, differences in GR were driven more by whole‐plant characteristics such as biomass fractions and total LA than individual leaf‐level traits such as photosynthetic rate or specific leaf area. Our results are most consistent with classical growth analysis—combining leaf traits with whole‐plant allocation to best predict growth. However, given that destructive biomass measures are often not feasible, applying easy‐to‐measure leaf traits associated with the CSR classification appear more predictive of whole‐plant growth than LES traits. Testing the generality of this result across additional taxa would further improve our ability to predict whole‐plant growth from functional traits across scales.

    

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