scholarly journals Plant–Microbe Interactions: From Genes to Ecosystems Using Populus as a Model System

2021 ◽  
pp. PBIOMES-01-20-0 ◽  
Author(s):  
Melissa A. Cregger ◽  
Dana L. Carper ◽  
Stephan Christel ◽  
Mitchel J. Doktycz ◽  
Jessy Labbé ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Microbial Community Composition ◽  
Model System ◽  
Natural Ecosystems ◽  
Sustainable Food ◽  
Perennial Plant ◽  
Excellent Model ◽  
Ecosystem Level ◽  
Microbe Interactions ◽  
Managed Ecosystems

Plant–microbe symbioses span a continuum from pathogenic to mutualistic, with functional consequences for both organisms in the symbiosis. In order to increase sustainable food and fuel production in the future, it is imperative that we harness these symbioses. The tree genus Populus is an excellent model system for studies examining plant–microbe interactions due to the wealth of genomic information available and the molecular tools that have been developed to manipulate Populus–microbe symbioses. In this review, we highlight how Populus can serve as a model system to explore plant–microbe interactions. Specifically, we highlight research linking Populus–microbe interactions from the gene to the ecosystem level. We explore why Populus is an excellent model for perennial plant systems, the molecular underpinnings of Populus–microbe interactions, how host genetics influence microbial community composition, and how microbial communities vary at fine spatial scales and between Populus spp. Furthermore, we explore how changes in the microbiome may affect ecosystem-level functions in managed and natural ecosystems. Understanding and manipulating these interactions in Populus has the potential to improve plant health and affect ecosystem sustainability and processes because Populus trees function as foundational species in many natural ecosystems and are also deployed in managed ecosystems for various agroforestry applications. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Consistent predictors of microbial community composition across scales in grasslands reveal low context-dependency

2021 ◽  
Author(s):  
Dajana Radujković ◽  
Sara Vicca ◽  
Margaretha van Rooyen ◽  
Peter Wilfahrt ◽  
Leslie Brown ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Spatial Scales ◽  
Regional Scale ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Plant Productivity ◽  
Context Dependency ◽  
Fungal Community Composition ◽  
Soil Microbial

Environmental circumstances shaping soil microbial communities have been studied extensively, but due to disparate study designs it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 sampled across regional plant productivity gradients) to examine i) if the same abiotic or biotic factors predict both large- and regional-scale patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently with regional plant productivity (low vs high) across different sites. We found that there is high congruence between predictors of microbial community composition across spatial scales; bacteria were predominantly associated with soil properties and fungi with plant community composition. Moreover, there was a microbial community signal that clearly distinguished high and low productivity soils that was shared across worldwide distributed grasslands suggesting that microbial assemblages vary predictably depending on grassland productivity.

Selective Bacterial Community Enrichment Between the Pitcher Plants Sarracenia Minor and Sarracenia Flava

2020 ◽  
Author(s):  
Nikolas M. Stasulli ◽  
Scott M. Yourstone ◽  
Ilon Weinstein ◽  
Elizabeth Ademski ◽  
Elizabeth A. Shank
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Prey Availability ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
Rrna Gene ◽  
Natural Ecosystems ◽  
Community Members ◽  
Pitcher Plants ◽  
Naturally Occurring

Abstract BackgroundThe interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cup-like leaf structures of some carnivorous plants, including the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava, when sampled at the same geographic location and time, cultivate unique microbiota; an indication of biotic selection of microbes due to eliminating many of the environmental variable present in other studies comparing samples harvested over several time points. ResultsDNA was extracted from the decomposing detritus trapped in the base of each Sarracenia leaf pitcher. We profiled a portion of the 16S rRNA gene across the bacterial community members present in this detritus using Illumina MiSeq technology. We identified a surprising amount of diversity within each pitcher, but also discovered that the two Sarracenia species each contained distinct, enriched microbial community members. This suggests a non-random establishment of microbial communities within these two Sarracenia species.ConclusionsOverall, our results indicate that microbial selection is occurring within the pitchers of these two closely related plant species, which is not due to factors such as geographic location, weather, or prey availability. This suggests that specific features of S. minor and S. flava may play a role in fostering specific insect-decomposing microbiomes. These naturally occurring microbial ecosystems can be developed to answer important questions about microbial community succession, disruption, and member contributions to the community. This study will help further establish carnivorous pitcher plants as a model system for studying confined, naturally occurring bacterial communities.

scholarly journals Baseline-Dependent Responses of Soil Organic Carbon Dynamics to Climate and Land Disturbances

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Zhengxi Tan ◽  
Shuguang Liu
Keyword(s):  
Land Use ◽  
Land Surface ◽  
Management Practices ◽  
C Sequestration ◽  
The United States ◽  
Natural Ecosystems ◽  
Organic C ◽  
Realistic Option ◽  
Managed Ecosystems ◽  
Land Use And Management

Terrestrial carbon (C) sequestration through optimizing land use and management is widely considered a realistic option to mitigate the global greenhouse effect. But how the responses of individual ecosystems to changes in land use and management are related to baseline soil organic C (SOC) levels still needs to be evaluated at various scales. In this study, we modeled SOC dynamics within both natural and managed ecosystems in North Dakota of the United States and found that the average SOC stock in the top 20 cm depth of soil lost at a rate of 450 kg C ha−1 yr−1in cropland and 110 kg C ha−1 yr−1in grassland between 1971 and 1998. Since 1998, the study area had become a SOC sink at a rate of 44 kg C ha−1 yr−1. The annual rate of SOC change in all types of lands substantially depends on the magnitude of initial SOC contents, but such dependency varies more with climatic variables within natural ecosystems and with management practices within managed ecosystems. Additionally, soils with high baseline SOC stocks tend to be C sources following any land surface disturbances, whereas soils having low baseline C contents likely become C sinks following conservation management.

Novel experimental methods for the identification of anoxic micro-niches in porous media.

2020 ◽  
Author(s):  
Giulia Ceriotti ◽  
Sergey Borisov ◽  
Pietro de Anna
Keyword(s):  
Porous Media ◽  
Solute Transport ◽  
Oxygen Concentration ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Quantitative Description ◽  
Concentration Field ◽  
Chemical Properties ◽  
Experimental Methodology ◽  
Shallow Subsurface

<div> <div> <div> <p>Porous media found in the shallow subsurface host an extremely heterogeneous environment arising from the complex coupling of abiotic (e.g. chemical reactions and anomalous solute transport) and biotic (e.g. metabolism and growth) processes. This heterogeneity is expected to characterize oxygen concentration distribution which is one of the major drivers for both abiotic and biotic redox reactions. Anoxic micro-niches, i.e. small portions of medium characterized by disproportionately different physical-chemical properties and microbial community composition compared to those characterizing the medium bulk, are expected to occur and persist even in averagely well-oxygenated porous media explaining macroscopic observed phenomena. However, the current lack of non-invasive technologies to observe the oxygen concentration field in porous media at spatial scales of interest for bacteria (i.e., 10 - 100 μm) structures still limits our ability to attain a quantitative description of anoxic micro-niches formation phenomenology in terms of their spatial distribution, average inter-niche distances, and proportion between oxygenated and anoxic pore-volume. This work presents the development, the implementation and preliminary as- sessment of a novel experimental methodology to observe oxygen concentration gradients and their evolution in space and time. This methodology combines the use of: a) PDMS microfluidics devices, which mimicking natural porous media geometries; b) planar transparent optodes which are fluorescent chemical sensors whose fluorescence intensity is quenched as a function of the oxygen concentration; and c) fully-automated microscope which allows to collect large images. The dynamics of oxy- gen concentration fields generated by pure physical processes are compared to those generated by the coupled effect of solute transport and the metabolism of aerobic bacteria. Our results allow to a) demonstrate the compatibility of microfluidics devices and optodes, b) highlight the strengths and challenges of the proposed novel methodology and c) reveal the ability of the planar optodes to capture fast evolving and sharp gradients associated with oxygen within porous media environment.</p> </div> </div> </div>

Achieving forest biodiversity outcomes across scales, jurisdictions and sectors with cycles of adaptive management integrated through criteria and indicators

2006 ◽  
Vol 82 (3) ◽  
pp. 321-334 ◽  
Author(s):  
B J McAfee ◽  
C. Malouin ◽  
N. Fletcher
Keyword(s):  
Adaptive Management ◽  
Sustainable Management ◽  
Sustainable Forest Management ◽  
Spatial Scales ◽  
Sustainable Use ◽  
Forest Biodiversity ◽  
Natural Ecosystems ◽  
Criteria And Indicators ◽  
Incomplete Knowledge ◽  
Canadian Council

The national forest strategy provided a model for Canada's international support for sustainable development, which later resulted in the development of a national biodiversity strategy. Adaptive management is a preferred approach for implementing such policies where incomplete knowledge and the highly variable dynamics associated with natural ecosystems are challenges. While the concept of adaptive management is embedded in various policies, complete implementation is only beginning in Canada. Case studies on adaptive management frameworks focusing on conservation and sustainable management of forest biodiversity compare how information has been integrated across spatial scales, jurisdictions and sectors of activity. To monitor progress in sustainable forest management, the Canadian Council of Forest Ministers established a framework of criteria and indicators in 1995. The potential for criteria and indicators reporting to drive cross-scale adaptive management of Canada's biological resources is discussed. Key words: forest biodiversity, conservation, sustainable use, criteria and indicators, adaptive management, monitoring

scholarly journals Lanai: A small, fast growing tomato variety is an excellent model system for studying geminiviruses

2018 ◽  
Vol 256 ◽  
pp. 89-99 ◽  
Author(s):  
C.A. Rajabu ◽  
G.G. Kennedy ◽  
J. Ndunguru ◽  
E.M. Ateka ◽  
F. Tairo ◽  
...  
Keyword(s):  
Model System ◽  
Tomato Variety ◽  
Fast Growing ◽  
Excellent Model

scholarly journals Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype

2009 ◽  
Vol 276 (1661) ◽  
pp. 1495-1506 ◽  
Author(s):  
William E Kunin ◽  
Philippine Vergeer ◽  
Tanaka Kenta ◽  
Matthew P Davey ◽  
Terry Burke ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Physical Distance ◽  
Population Variation ◽  
Regional Patterns ◽  
Range Margin ◽  
Arabidopsis Lyrata ◽  
Perennial Plant ◽  
Temperature Regimes ◽  
Population Structures ◽  
Genetic Profiles

Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent.

Man and Forests: A Case-study from the Dry Tropics of India

1989 ◽  
Vol 16 (2) ◽  
pp. 129-136 ◽  
Author(s):  
V.P. Singh ◽  
J.S. Singh
Keyword(s):  
Crop Production ◽  
Life Cycles ◽  
Natural Forest ◽  
Agricultural Activity ◽  
Natural Ecosystems ◽  
Fuel Wood ◽  
Dry Land ◽  
Total Failure ◽  
Ecosystem Level ◽  
Land Farming

The present study analyses the energy-budget of ‘village ecosystems’ in a dry tropical environment. These systems depend to a great extent on the surrounding natural forest/savanna ecosystems. Accordingly the objectives of the study were to quantify (i) the energy efficiency of rain-fed agriculture at the ecosystem level, and (ii) the indirect impact of agricultural activity on the surrounding forest/savanna ecosystems.Agronomic output from farming is not sufficient to meet the food-energy requirements of the villagers, hence 27.0 to 51.0% of the requirement is met from outside markets. Operation of the agro-ecosystems involved requires a considerable amount of subsidy from the surrounding forest/savanna ecosystems in terms of fodder and fuel-wood. About 81 to 100% of the fuel needs, and 80–87% of the fodder needs, are met from the natural forest/savanna ecosystems. Thus, for each unit of energy obtained in agronomic yield (including milk), 3.1 units of energy are expended from the surrounding natural ecosystems in the form of fodder and fuel-wood.The erratic and ill-distributed nature of monsoon rains results in moisture deficit which affects the crop production in dry-land farming, causing partial or total failure of the crops. For achieving increased and stable agronomic production under rain-fed conditions, improved dry-land farming techniques have to be applied. Some of these techniques are: (1) introduction of crops and varieties that would be capable of maturing in a period of 90–100 days, and adequate use of appropriate fertilizers; (2) planned rain-water management including storage of surface runoff; and (3) practices of intercropping with crops of longer duration than those currently grown, having slow growth-rates in the early part of their life-cycles.

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