scholarly journals Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dong Li ◽  
Haowei Ni ◽  
Shuo Jiao ◽  
Yahai Lu ◽  
Jizhong Zhou ◽  
...  
Keyword(s):  
Species Interactions ◽  
Functional Significance ◽  
Abiotic Factors ◽  
Mean Annual Temperature ◽  
Rice Paddies ◽  
Asian Continent ◽  
Local Networks ◽  
Methane Generation ◽  
Complex Interactions ◽  
Archaeal Communities

Abstract Background Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. Results The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. Conclusions These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions.

scholarly journals Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review

2021 ◽  
Vol 9 (2) ◽  
pp. 417
Author(s):  
Sherli Koshy-Chenthittayil ◽  
Linda Archambault ◽  
Dhananjai Senthilkumar ◽  
Reinhard Laubenbacher ◽  
Pedro Mendes ◽  
...  
Keyword(s):  
Species Interactions ◽  
Computational Models ◽  
Human Microbiome ◽  
Agent Based Modeling ◽  
Autonomous Agent ◽  
Agent Based Models ◽  
Agent Based ◽  
Complex Interactions ◽  
Mucosal Surfaces ◽  
Living Organisms

The human microbiome has been a focus of intense study in recent years. Most of the living organisms comprising the microbiome exist in the form of biofilms on mucosal surfaces lining our digestive, respiratory, and genito-urinary tracts. While health-associated microbiota contribute to digestion, provide essential nutrients, and protect us from pathogens, disturbances due to illness or medical interventions contribute to infections, some that can be fatal. Myriad biological processes influence the make-up of the microbiota, for example: growth, division, death, and production of extracellular polymers (EPS), and metabolites. Inter-species interactions include competition, inhibition, and symbiosis. Computational models are becoming widely used to better understand these interactions. Agent-based modeling is a particularly useful computational approach to implement the various complex interactions in microbial communities when appropriately combined with an experimental approach. In these models, each cell is represented as an autonomous agent with its own set of rules, with different rules for each species. In this review, we will discuss innovations in agent-based modeling of biofilms and the microbiota in the past five years from the biological and mathematical perspectives and discuss how agent-based models can be further utilized to enhance our comprehension of the complex world of polymicrobial biofilms and the microbiome.

Spatial Patterns and Drivers of Soil Chemical Properties in a Typical Hickory Plantation

2021 ◽  
Author(s):  
Mengjiao Sun ◽  
Enqing Hou ◽  
Jiasen Wu ◽  
Jianqin Huang ◽  
Xingzhao Huang
Keyword(s):  
Random Forest ◽  
Soil Nutrients ◽  
Spatial Patterns ◽  
Abiotic Factors ◽  
Soil Nutrient ◽  
Parent Material ◽  
Mean Annual Precipitation ◽  
Nutrient Concentrations ◽  
Available Phosphorus ◽  
Mean Annual Temperature

Abstract Background: Soil nutrients play critical roles in regulating and improving the sustainable development of economic forests. Consequently, an elucidation of the spatial patterns and drivers of soil nutrients in these forests is fundamental to their management. For this study, we collected 314 composite soils at a 0-30 cm depth from a typical hickory plantation in Lin 'an, Zhejiang Province, China. We determined the concentrations of macronutrients (i.e., soil organic carbon, hydrolyzed nitrogen, available phosphorus, and available potassium) and micronutrients (i.e., iron, manganese, zinc, and copper.) of the soils. We employed random forest analysis to quantify the relative importance of soil-forming factors to predict the soil nutrient concentrations, which could then be extrapolated to the entire hickory region. Results: Random forest models explained 61%–88% of the variations in soil nutrient concentrations. The mean annual temperature and mean annual precipitation were the most important predictor of soil macronutrient and micronutrient concentrations. Moreover, parent material was another key predictor of soil available phosphorus and micronutrient concentrations. Mapping results demonstrated the importance of climate in controlling the spatial distribution of soil nutrient concentrations at finer scales, as well as the effect of parent material, topography, stand structure, and management measures of hickory plantations. Conclusions: Our study highlights the biotic factors, abiotic factors, and management factors control over soil macronutrient and micronutrient concentrations, which have significant implications for the sustainability of soil nutrients in forest plantations.

Answers.

2020 ◽  
pp. 179-214
Author(s):  
Paul A. Rees
Keyword(s):  
Community Ecology ◽  
Population Ecology ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Multiple Choice ◽  
Ecological Genetics ◽  
Major Topic ◽  
Production Ecology ◽  
Material Cycles ◽  
Ecological Methods

Abstract A multiple choice question has a stem (the 'question'), a key (the 'answer') and a number of distracters (wrong answers intended to distract the student from the key). This part of the book contains the key to each question along with a brief explanation of why this is correct and, in some cases, what the distracters mean. The questions are grouped into 10 major topic areas: (1) The history and foundations of ecology, (2) Abiotic factors and environmental monitoring, (3) Taxonomy and biodiversity, (4) Energy flow and production ecology, (5) Nutrient and material cycles, (6) Ecophysiology, (7) Population ecology, (8) Community ecology and species interactions, (9) Ecological genetics and evolution, (10) Ecological methods and statistics.

Complex interactions of biotic and abiotic factors shape venom phenotypes in the Western rattlesnakes

Toxicon ◽  
2020 ◽  
Vol 182 ◽  
pp. S8-S9
Author(s):  
S.P. Mackessy ◽  
C.F. Smith ◽  
A.J. Saviola ◽  
D. Schield ◽  
B.W. Perry ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Biotic And Abiotic Factors ◽  
Complex Interactions

scholarly journals Aridity weakens population-level effects of multiple species interactions on Hibiscus meyeri

2017 ◽  
Vol 115 (3) ◽  
pp. 543-548 ◽  
Author(s):  
Allison M. Louthan ◽  
Robert M. Pringle ◽  
Jacob R. Goheen ◽  
Todd M. Palmer ◽  
William F. Morris ◽  
...  
Keyword(s):  
Population Growth ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Population Level ◽  
Distinct Species ◽  
High Elevation ◽  
Relative Strength ◽  
Herbaceous Plant ◽  
Species Abundances ◽  
Multiple Species

Predicting how species’ abundances and ranges will shift in response to climate change requires a mechanistic understanding of how multiple factors interact to limit population growth. Both abiotic stress and species interactions can limit populations and potentially set range boundaries, but we have a poor understanding of when and where each is most critical. A commonly cited hypothesis, first proposed by Darwin, posits that abiotic factors (e.g., temperature, precipitation) are stronger determinants of range boundaries in apparently abiotically stressful areas (“stress” indicates abiotic factors that reduce population growth), including desert, polar, or high-elevation environments, whereas species interactions (e.g., herbivory, competition) play a stronger role in apparently less stressful environments. We tested a core tenet of this hypothesis—that population growth rate is more strongly affected by species interactions in less stressful areas—using experimental manipulations of species interactions affecting a common herbaceous plant, Hibiscus meyeri (Malvaceae), across an aridity gradient in a semiarid African savanna. Population growth was more strongly affected by four distinct species interactions (competition with herbaceous and shrubby neighbors, herbivory, and pollination) in less stressful mesic areas than in more stressful arid sites. However, contrary to common assumptions, this effect did not arise because of greater density or diversity of interacting species in less stressful areas, but rather because aridity reduced sensitivity of population growth to these interactions. Our work supports classic predictions about the relative strength of factors regulating population growth across stress gradients, but suggests that this pattern results from a previously unappreciated mechanism that may apply to many species worldwide.

Complex Interactions between Biotic and Abiotic Factors: Effects on Mycophagous Fly Communities

Oikos ◽  
1994 ◽  
Vol 69 (2) ◽  
pp. 277 ◽  
Author(s):  
Wade B. Worthen ◽  
Sara Mayrose ◽  
R. Gayle Wilson
Keyword(s):  
Abiotic Factors ◽  
Biotic And Abiotic Factors ◽  
Complex Interactions

scholarly journals Influence of abiotic factors on CO2-gas exchange of Pinus pallasiana, Juniperus excelsa and Arbutus andrachne

2020 ◽  
Vol 224 ◽  
pp. 04017
Author(s):  
S Korsakova ◽  
Y Plugatar ◽  
A Pashtetsky ◽  
O Ilnitsky
Keyword(s):  
Shade Tolerance ◽  
Abiotic Factors ◽  
Incident Light ◽  
Photosynthetic Apparatus ◽  
Climatic Conditions ◽  
Co2 Gas ◽  
Rectangular Hyperbola ◽  
Complex Interactions ◽  
Juniperus Excelsa ◽  
Lower Capacity

The complex interactions among environmental factors as incident light, temperature and soil water content create the need for used physiology-based models which describe plants performance under current and changing climatic conditions. In the present work the net photosynthetic rate of Pinus pallasiana D. Don, Juniperus excelsa M.Bieb. and Arbutus andrachne L. was modeled as a function of light irradiance using the modified rectangular hyperbola model, which is capable of describing the photoinhibition by the non-rectangular hyperbola function. A comparative assessment of the adaptive response of the photosynthetic apparatus plants on the effect of abiotic factors and their strategies in maintaining an optimal water balance in accordance with environmental conditions has been performed. The parameters of light curves of photosynthesis under conditions of full sunlight, moderate shading and drought are determined. In relation to light, Pinus pallasiana is characterized by wider ecological amplitude compared to Juniperus excelsa and Arbutus andrachne. Inefficient use of low-intensity of photosynthetically active radiation by immature plants Pinus pallasiana and Juniperus excelsa indicates poor shade tolerance and inability to resume in shade-type forests. Due to the low plasticity to changes in the light regime, Arbutus andrachne L. may experience a significant lack of light in strong shading. Arbutus andrachne has the highest ability to actively rearrange water regime in accordance with its external moisture supply, which causes the highest drought resistance, and Juniperus excelsa has a slightly lower capacity. Tolerance to hydrothermal stress in Pinus pallasiana is significantly lower than in Arbutus andrachne and Juniperus excelsa.

scholarly journals Climate change and local host availability drive the northern range boundary in the rapid northward expansion of the eastern giant swallowtail butterfly

2019 ◽  
Author(s):  
J. Keaton Wilson ◽  
Nicolas Casajus ◽  
Rebecca A. Hutchinson ◽  
Kent P. McFarland ◽  
Jeremy T. Kerr ◽  
...  
Keyword(s):  
North America ◽  
Range Expansion ◽  
Host Plants ◽  
Spatial Scales ◽  
Abiotic Factors ◽  
Mean Annual Temperature ◽  
Suitable Habitat ◽  
Distribution Models ◽  
Swallowtail Butterfly ◽  
Bioclimatic Variables

ABSTRACTAimsSpecies distributions result from both biotic and abiotic interactions across large spatial scales. The interplay of these interactions as climate changes quickly has been understudied, particularly in herbivorous insects. Here, we investigate the relative impacts these influences on the putative northern range expansion of the giant swallowtail butterfly in North America.LocationNorth America.Time period1959-2018.Major taxa studiedEastern Giant swallowtail, Papilio cresphontes (Lepidoptera: Papilionidae); common hop tree, Ptelea trifoliata; common prickly ash, Zanthoxylum americanum; southern prickly ash, Zanthoxylum clava-herculis (Saphidales: Rutaceae).MethodsWe used data from museum collections and citizen science repositories to generate species distribution models. Distribution models were built for each species over two time periods (T1 = 1959-1999; T2 = 2000-2018).ResultsModels for P. cresphontes and associated host plants had high predictive accuracy on spatially-explicit test data (AUC 0.810-0.996). Occurrence data align with model outputs, providing strong evidence for a northward range expansion in the last 19 years (T2) by P. cresphontes. Host plants have shifted in more complex ways, and result in a change in suitable habitat for P. cresphontes in its historic range. P. cresphontes has a northern range which now closely aligns with its most northern host plant - continued expansion northward is unlikely, and historic northern range limits were likely determined by abiotic, not biotic, factors.Main conclusionsBiotic and abiotic factors have driven the rapid northern range expansion in the giant swallowtail butterfly across North America in the last 20 years. A number of bioclimatic variables are correlated with this expansion, notably an increase in mean annual temperature and minimum winter temperature. We predict a slowing of northward range expansion in the next 20-50 years as butterflies are now limited by the range of host plants, rather than abiotic factors.

scholarly journals Formation of multi-species biofilms and their resistance to disinfectants in food processing environments: A review

2021 ◽  
Author(s):  
Ailing Guo ◽  
Qun Li ◽  
Ling Liu ◽  
Xinshuai Zhang ◽  
Wukang Liu ◽  
...  
Keyword(s):  
Food Safety ◽  
Quorum Sensing ◽  
Food Processing ◽  
Species Interactions ◽  
Extracellular Polymeric Substances ◽  
Resistance Mechanisms ◽  
Signal Molecules ◽  
Complex Interactions ◽  
Food Safety And Quality

In food processing environments, various microorganisms can adhere and aggregate on the surface of equipment, resulting in the formation of multi-species biofilms. Complex interactions among microorganisms may affect the formation of multi-species biofilms and their resistance to disinfectants, which are food safety and quality concerns. This paper reviews the various interactions among microorganisms in multi-species biofilms, including competitive, cooperative and neutral interactions. Then, the preliminary mechanisms underlying the formation of multi-species biofilms are discussed in relation to factors, such as quorum sensing (QS) signal molecules, extracellular polymeric substances (EPS) and biofilm-regulated genes. Finally, the resistance mechanisms of common contaminating microorganisms to disinfectants in food processing environments are also summarized. This review is expected to facilitate a better understanding of inter-species interactions, and provide some implications for the control of multi-species biofilms in food processing.

scholarly journals High-order interactions dominate the functional landscape of microbial consortia

2018 ◽  
Author(s):  
Alicia Sanchez-Gorostiaga ◽  
Djordje Bajić ◽  
Melisa L. Osborne ◽  
Juan F. Poyatos ◽  
Alvaro Sanchez
Keyword(s):  
Species Interactions ◽  
Species Traits ◽  
High Order ◽  
Microbial Consortia ◽  
Order Effects ◽  
High Performing ◽  
Community Function ◽  
Functional Interactions ◽  
Complex Interactions ◽  
And Function

AbstractUnderstanding the link between community composition and function is a major challenge in microbial ecology, with implications for the management of natural microbiomes and the design of synthetic consortia. For this purpose, it is critical to understand the extent to which community functions and properties can be predicted from species traits and what role is played by complex interactions. Inspired by the study of complex genetic interactions and fitness landscapes, here we have examined how the amylolytic function of combinatorial assemblages of seven starch-degrading soil bacteria depends on the functional contributions from each species and their interactions. Filtering our experimental results through the theory of enzyme kinetics, we show that high-order functional interactions dominate the amylolytic rate of our consortia, even though this function is biochemically simple, redundantly distributed in the community, and additive in the absence of inter-species interactions. As the community grows in size, the contribution of high-order functional interactions grows too, making the community function increasingly unpredictable. We can explain the prevalence of high order effects and their sign from the redundancy of ecological interactions in the network, in particular from redundant facilitation towards a high-performing community member. Our results suggest that even simple functions can be dominated by complex interactions, posing challenges for the predictability and bottom-up engineering of ecosystem function in complex multi-species communities.

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