scholarly journals Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis

2021 ◽  
Vol 146 ◽  
pp. 106234
Author(s):  
Maria Luíza S. Suhadolnik ◽  
Patrícia S. Costa ◽  
Giovanni M. Castro ◽  
Francisco P. Lobo ◽  
Andréa M.A. Nascimento
Keyword(s):  
Meta Analysis ◽  
Environmental Drivers ◽  
Iron Redox

scholarly journals Systematic review and meta-analysis of 50 years of coral disease research visualized through the scope of network theory

2018 ◽  
Author(s):  
Luis M. Montilla ◽  
Alfredo Ascanio ◽  
Alejandra Verde ◽  
Aldo Croquer
Keyword(s):  
Research Effort ◽  
Coral Disease ◽  
Meta Analysis ◽  
Limited Range ◽  
Environmental Drivers ◽  
Network Nodes ◽  
Host Genus ◽  
Disease Research ◽  
Multiple Processes ◽  
Black Band

AbstractCoral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. To gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: 1) studied disease(s); 2) host genus; 3) marine ecoregion(s) associated with the study site; and 4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g. bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research.

scholarly journals A meta-analysis on environmental drivers of marine phytoplankton C : N : P

2020 ◽  
Vol 17 (11) ◽  
pp. 2939-2954 ◽  
Author(s):  
Tatsuro Tanioka ◽  
Katsumi Matsumoto
Keyword(s):  
Inorganic Nitrogen ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Critical Role ◽  
Inorganic Phosphorus ◽  
Marine Phytoplankton ◽  
Environmental Drivers ◽  
Carbon Export ◽  
Elemental Stoichiometry ◽  
Eukaryotic Phytoplankton

Abstract. The elemental stoichiometry of marine phytoplankton plays a critical role in global biogeochemical cycles through its impact on nutrient cycling, secondary production, and carbon export. Although extensive laboratory experiments have been carried out over the years to assess the influence of different environmental drivers on the elemental composition of phytoplankton, a comprehensive quantitative assessment of the processes is still lacking. Here, we synthesized the responses of P:C and N:C ratios of marine phytoplankton to five major drivers (inorganic phosphorus, inorganic nitrogen, inorganic iron, irradiance, and temperature) by a meta-analysis of experimental data across 366 experiments from 104 journal articles. Our results show that the response of these ratios to changes in macronutrients is consistent across all the studies, where the increase in nutrient availability is positively related to changes in P:C and N:C ratios. We found that eukaryotic phytoplankton are more sensitive to the changes in macronutrients compared to prokaryotes, possibly due to their larger cell size and their abilities to regulate their gene expression patterns quickly. The effect of irradiance was significant and constant across all studies, where an increase in irradiance decreased both P:C and N:C. The P:C ratio decreased significantly with warming, but the response to temperature changes was mixed depending on the culture growth mode and the growth phase at the time of harvest. Along with other oceanographic conditions of the subtropical gyres (e.g., low macronutrient availability), the elevated temperature may explain why P:C is consistently low in subtropical oceans. Iron addition did not systematically change either P:C or N:C. Overall, our findings highlight the high stoichiometric plasticity of eukaryotes and the importance of macronutrients in determining P:C and N:C ratios, which both provide us insights on how to understand and model plankton diversity and productivity.

scholarly journals Dominance structure of assemblages is regulated over a period of rapid environmental change

2018 ◽  
Vol 14 (6) ◽  
pp. 20180187 ◽  
Author(s):  
Faith A. M. Jones ◽  
Anne E. Magurran
Keyword(s):  
Dominant Species ◽  
Meta Analysis ◽  
Environmental Drivers ◽  
Systematic Change ◽  
Ecosystem Responses ◽  
Multiple Components ◽  
Dominance Structure ◽  
Biodiversity Change ◽  
Permutation Models ◽  
Assemblage Size

Ecological assemblages are inherently uneven, with numerically dominant species contributing disproportionately to ecosystem services. Marked biodiversity change due to growing pressures on the world's ecosystems is now well documented. However, the hypothesis that dominant species are becoming relatively more abundant has not been tested. We examined the prediction that the dominance structure of contemporary communities is shifting, using a meta-analysis of 110 assemblage timeseries. Changes in relative and absolute dominance were evaluated with mixed and cyclic-shift permutation models. Our analysis uncovered no evidence of a systematic change in either form of dominance, but established that relative dominance is preserved even when assemblage size (total N ) changes. This suggests that dominance structure is regulated alongside richness and assemblage size, and highlights the importance of investigating multiple components of assemblage diversity when evaluating ecosystem responses to environmental drivers.

scholarly journals Global coral reef ecosystems exhibit declining calcification and increasing primary productivity

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Kay L. Davis ◽  
Andrew P. Colefax ◽  
James P. Tucker ◽  
Brendan P. Kelaher ◽  
Isaac R. Santos
Keyword(s):  
Coral Reef ◽  
Multiple Stressors ◽  
Coral Cover ◽  
Meta Analysis ◽  
Environmental Drivers ◽  
Spatiotemporal Trends ◽  
Coral Reef Resilience ◽  
Coral Reef Ecosystems ◽  
Seawater Carbonate Chemistry ◽  
Organic Productivity

AbstractLong-term coral reef resilience to multiple stressors depends on their ability to maintain positive calcification rates. Estimates of coral ecosystem calcification and organic productivity provide insight into the environmental drivers and temporal changes in reef condition. Here, we analyse global spatiotemporal trends and drivers of coral reef calcification using a meta-analysis of ecosystem-scale case studies. A linear mixed effects regression model was used to test whether ecosystem-scale calcification is related to seasonality, methodology, calcifier cover, year, depth, wave action, latitude, duration of data collection, coral reef state, Ωar, temperature and organic productivity. Global ecosystem calcification estimated from changes in seawater carbonate chemistry was driven primarily by depth and benthic calcifier cover. Current and future declines in coral cover will significantly affect the global reef carbonate budget, even before considering the effects of sub-lethal stressors on calcification rates. Repeatedly studied reefs exhibited declining calcification of 4.3 ± 1.9% per year (x̄  = 1.8 ± 0.7 mmol m−2 d−1 yr−1), and increasing organic productivity at 3.0 ± 0.8 mmol m−2 d−1 per year since 1970. Therefore, coral reef ecosystems are experiencing a shift in their essential metabolic processes of calcification and photosynthesis, and could become net dissolving worldwide around 2054.

scholarly journals Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles

2020 ◽  
Author(s):  
Antoni Luque ◽  
Cynthia Silveira
Keyword(s):  
Microbial Communities ◽  
Meta Analysis ◽  
Community Diversity ◽  
Biophysical Model ◽  
Environmental Drivers ◽  
Lambda Phage ◽  
Human Gut ◽  
Poor Growth ◽  
Phage Adsorption ◽  
Adsorption Rates

AbstractTemperate phages can integrate in their bacterial host genome to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbial-dense environment of the mammalian-gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored in microbial communities with low densities. Here we hypothesized that phage coinfections—the most studied molecular mechanism of lysogeny in lambda phage—increases at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection and stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from marine and gut microbiomes. Based on lambda experiments, a Poisson process assessed the probability of lysogeny via coinfection in these ecosystems. In 90% of the sampled marine ecosystems, lysogeny stayed below 10% of the bacterial community. In contrast, 25% of the sampled gut communities stayed above 25% of lysogeny, representing an estimated nine trillion lysogens formed via phage coinfection in the human gut every day. The prevalence of lysogeny in the gut was a consequence of the higher densities and faster adsorption rates. In marine communities, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitments times. Our study suggests that physical mechanisms can favor coinfection and cause lysogeny at poor growth conditions (long commitment times) and in rich environments (high densities and adsorption rates).ImportancePhage integration in bacterial genomes manipulate microbial dynamics from the oceans to the human gut. This phage-bacteria interaction, called lysogeny, is well-studied in laboratory models, but its environmental drivers remain unclear. Here we quantified the frequency of lysogeny via phage coinfection—the most studied mechanism of lysogeny—by developing a biophysical model that incorporated a meta-analysis of the properties of marine and gut microbiomes. Lysogeny was found to be more frequent in high-productive environments like the gut, due to higher phage and bacterial densities and faster phage adsorption rates. At low cell densities, lysogeny via coinfection was possible for hosts with long duplication times. Our research bridges the molecular understanding of lysogeny with the ecology of complex microbial communities.

scholarly journals Modelling for risk and biosecurity related to forest health

2020 ◽  
Vol 4 (5) ◽  
pp. 485-495 ◽  
Author(s):  
Christelle Robinet ◽  
Robbert van den Dool ◽  
Dorian Collot ◽  
Jacob C. Douma
Keyword(s):  
Native Species ◽  
Temporal Dynamics ◽  
Risk Mitigation ◽  
Meta Analysis ◽  
Forest Health ◽  
Species Traits ◽  
Process Models ◽  
Environmental Drivers ◽  
Distribution Models ◽  
Inference Models

Modelling the invasion and emergence of forest pests and pathogens (PnPs) is necessary to quantify the risk levels for forest health and provide key information for policy makers. Here, we make a short review of the models used to quantify the invasion risk of exotic species and the emergence risk of native species. Regarding the invasion process, models tackle each invasion phase, e.g. pathway models to describe the risk of entry, species distribution models to describe potential establishment, and dispersal models to describe (human-assisted) spread. Concerning the emergence process, models tackle each process: spread or outbreak. Only a few spread models describe jointly dispersal, growth, and establishment capabilities of native species while some mechanistic models describe the population temporal dynamics and inference models describe the probability of outbreak. We also discuss the ways to quantify uncertainty and the role of machine learning. Overall, promising directions are to increase the models’ genericity by parameterization based on meta-analysis techniques to combine the effect of species traits and various environmental drivers. Further perspectives consist in considering the models’ interconnection, including the assessment of the economic impact and risk mitigation options, as well as the possibility of having multi-risks and the reduction in uncertainty by collecting larger fit-for-purpose datasets.

Reconsidering the impossible — linking environmental drivers to growth, mortality, and recruitment of fish

2016 ◽  
Vol 73 (2) ◽  
pp. 205-215 ◽  
Author(s):  
Pierre Pepin
Keyword(s):  
Early Life ◽  
Stock Assessment ◽  
Meta Analysis ◽  
Trophic Relationships ◽  
Environmental Drivers ◽  
Limited Information ◽  
Fisheries Science ◽  
Assessment Time ◽  
Stock Recruitment ◽  
New Research

After a century of research into the drivers of early life (EL) growth and mortality, fisheries science has acquired limited capacity to predict future recruitment. A meta-analysis of stock assessment time series revealed that it may be difficult to identify stock– or environmental–recruitment drivers given limited variability in spawner biomass, recruitment, and survivorship in most populations. In nearly 50% of the stocks, there was limited information at low spawner biomass, limiting the reliability of fits to stock–recruitment models. Furthermore, variations in survivorship in 50% of year-classes resulted in less than a 2.5-fold change in recruitment. Simulations of three scenarios of change in EL growth and mortality rates demonstrated that they must covary positively to reproduce variations in survivorship consistent with observations. The potentially limited reliability of stock–recruitment relationships to predict year-class strength in many stocks and the low variability in survivorship in a large proportion of year-classes has important implications for the development of projections of stock productivity used in scientific advice. Furthermore, if a positive growth–mortality relationship underlies variations in survivorship, new research approaches are required to understand the trophic relationships that govern the dynamics of early life stages of fish and patterns of recruitment variability.

scholarly journals Global tree intrinsic water use efficiency is enhanced by increased atmospheric CO2 and modulated by climate and plant functional types

2021 ◽  
Vol 118 (7) ◽  
pp. e2014286118
Author(s):  
Justin M. Mathias ◽  
Richard B. Thomas
Keyword(s):  
Water Use Efficiency ◽  
Water Use ◽  
Meta Analysis ◽  
Net Photosynthesis ◽  
Environmental Drivers ◽  
Carbon Gain ◽  
Carbon And Oxygen Isotopes ◽  
Functional Types ◽  
Intrinsic Water Use Efficiency ◽  
Use Efficiency

We conducted a meta-analysis of carbon and oxygen isotopes from tree ring chronologies representing 34 species across 10 biomes to better understand the environmental drivers and physiological mechanisms leading to historical changes in tree intrinsic water use efficiency (iWUE), or the ratio of net photosynthesis (Anet) to stomatal conductance (gs), over the last century. We show a ∼40% increase in tree iWUE globally since 1901, coinciding with a ∼34% increase in atmospheric CO2 (Ca), although mean iWUE, and the rates of increase, varied across biomes and leaf and wood functional types. While Ca was a dominant environmental driver of iWUE, the effects of increasing Ca were modulated either positively or negatively by climate, including vapor pressure deficit (VPD), temperature, and precipitation, and by leaf and wood functional types. A dual carbon–oxygen isotope approach revealed that increases in Anet dominated the observed increased iWUE in ∼83% of examined cases, supporting recent reports of global increases in Anet, whereas reductions in gs occurred in the remaining ∼17%. This meta-analysis provides a strong process-based framework for predicting changes in tree carbon gain and water loss across biomes and across wood and leaf functional types, and the interactions between Ca and other environmental factors have important implications for the coupled carbon–hydrologic cycles under future climate. Our results furthermore challenge the idea of widespread reductions in gs as the major driver of increasing tree iWUE and will better inform Earth system models regarding the role of trees in the global carbon and water cycles.

scholarly journals Systematic review and meta-analysis of 50 years of coral disease research visualized through the scope of network theory

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7041 ◽  
Author(s):  
Luis M. Montilla ◽  
Alfredo Ascanio ◽  
Alejandra Verde ◽  
Aldo Croquer
Keyword(s):  
Research Effort ◽  
Coral Disease ◽  
Meta Analysis ◽  
Limited Range ◽  
Environmental Drivers ◽  
Network Nodes ◽  
Host Genus ◽  
Disease Research ◽  
Multiple Processes ◽  
Black Band

Coral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. In order to gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: (1) studied disease(s); (2) host genus; (3) marine ecoregion(s) associated with the study site; and (4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g., bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research.

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