TY - CHAP T1 - Toward cyber-eco systems: networked sensing, inference and control for ecological and agricultural systems. T2 - Handbook of dynamic data driven applications systems, Y1 - 2023 A1 - Heinrich, Paul L A1 - Flikkema, Paul G A1 - Darema F A1 - Blasch EP A1 - Aved AJ KW - Cyber-eco systems KW - Ecological sensing KW - Precision agriculture KW - Sensor/actuator networks KW - Wireless AB - New applications are motivating and informing the design of sen- sor/actuator networks, and, more broadly, distributed intelligent systems. Key to the success of these systems is the Dynamic Data Driven Application System (DDDAS) paradigm, characterized by the ability of the system to ingest new data and in turn steer the collection of that data. Our knowledge of many phys- ical systems is uncertain, so that sensing and actuation must be mediated by inference of the structure and parameters of physical-system models. One ap- plication domain of rapidly growing interest is ecological research and agricul- tural systems, motivated by the need to understand plant survival and growth as a function of genetics, environment, and climate. For these applications, we must develop cyber-eco systems that infer coupled dynamic data-driven pre- dictive models of plant growth dynamics in response to weather and climate drivers that allow incorporation of uncertainty. This Chapter describes the algorithms and system architecture we have developed for this class of cyber- eco systems, including sensor/actuator node design, site-level networking, data assimilation, inference, and distributed control. Among its innovations are a modular, parallel-processing node hardware design allowing real-time process- ing and heterogeneous nodes, energy-aware hardware/software design, and a networking protocol that builds in trade-o s between energy conservation and latency. Our implementations include experimental networks in an Eastern USA forest environment and an operational distributed system, the Southwest Experimental Garden Array, consisting of geographically-distributed outdoor gardens on an elevational gradient of over 1500 m in Arizona, USA. Finally, we summarize results for fine-scale inference of soil moisture and control of irrigation. JF - Handbook of dynamic data driven applications systems, PB - Springer, Cham. VL - 2 ER - TY - JOUR T1 - Tree genetics defines fungal partner communities that may confer drought tolerance. JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES Y1 - 2017 A1 - Gehring, C.A. A1 - Sthultz, C.M. A1 - Flores-Rentería, L. A1 - A.V. Whipple A1 - T.G. Whitham AB -

Plant genetic variation and soil microorganisms are individually known to influence plant responses to climate change, but the interactive effects of these two factors are largely unknown. Using long-term observational studies in the field and common garden and greenhouse experiments of a foundation tree species (Pinus edulis) and its mutualistic ectomycorrhizal fungal (EMF) associates, we show that EMF community composition is under strong plant genetic control. Seedlings acquire the EMF community of their seed source trees (drought tolerant vs. drought intolerant), even when exposed to inoculum from the alternate tree type. Drought-tolerant trees had 25% higher growth and a third the mortality of drought-intolerant trees over the course of 10 y of drought in the wild, traits that were also observed in their seedlings in a common garden. Inoculation experiments show that EMF communities are critical to drought tolerance. Drought-tolerant and drought-intolerant seedlings grew similarly when provided sterile EMF inoculum, but drought-tolerant seedlings grew 25% larger than drought-intolerant seedlings under dry conditions when each seedling type developed its distinct EMF community. This demonstration that particular combinations of plant genotype and mutualistic EMF communities improve the survival and growth of trees with drought is especially important, given the vulnerability of forests around the world to the warming and drying conditions predicted for the future.

VL - 114 UR - https://www.pnas.org/content/114/42/11169 IS - 42 ER - TY - JOUR T1 - Trees harness the power of microbes to survive climate change JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES Y1 - 2017 A1 - Jennifer A. Lau A1 - Jay T. Lennon A1 - Katy D. Heath AB -

Microorganisms are the most abundant and diverse taxa on Earth. They have the ability to tolerate extreme environments, catalyze a range of metabolic functions, and rapidly evolve in response to changing environmental conditions. Imagine if plants and animals could harness these powers. In fact, microorganisms confer numerous benefits to plants and animals. For example, microorganisms in the mammalian gut improve nutrition, reduce susceptibility to disease, and even alter host behavior (1). Some of the most complex microbiomes are found in soils, where they are responsible for nutrient cycling, crop yield, and carbon sequestration (2). In some cases, soil microbes can even rescue plants from the negative consequences of climate change (3). If plants and animals can build associations with specific microbial members that maximize benefits, then harnessing microbial powers may provide rapid and efficient solutions to the challenges resulting from global change.

In PNAS, Gehring et al. (4) show that the relationship between soil microbial communities and plants is not a fortunate coincidence. Instead, some pinyon pine genotypes form associations with different belowground ectomycorrhizal fungal (EMF) communities that help them contend with drought. These EMF communities were responsible for the observed difference in drought tolerance between host tree genotypes. Because these microbial communities are, at least partially, under plant genetic control, EMF community composition is an extended phenotype of the host tree and potentially a mode of adaptation to the increased drought stress pinyon pines face in a changing climate. Given the vast array of biogeochemical and metabolic functions in the microbial arsenal, if similarly tight linkages occur between diverse soil bacterial and fungal communities and host plant genotypes, then host plants may possess a powerful tactic for adapting to environmental change.

VL - 114 UR - https://www.pnas.org/content/114/42/11009 IS - 42 ER - TY - CONF T1 - Taxon-specific microbial activities explain soil carbon cycling dynamics. T2 - Ecological Society of America Y1 - 2016 A1 - Morrissey,EM A1 - RL Mau A1 - Schwartz,E A1 - Caporaso,JG A1 - P Dijkstra A1 - McHugh,T A1 - Marks,JC A1 - Price,LB A1 - Liu,CM A1 - Hungate,BA AB -

Morrissey, E.M., Mau, R.L., Schwartz, E., Caporaso, J.G., Dijkstra, P.,McHugh, T., Marks, J.C., Price, L.B., Liu, C.M. and Hungate, B.A. (2016). Taxon-specific microbial activities explain soil carbon cycling dynamics. ESA August 7-12, Fort Lauderdale.

JF - Ecological Society of America T3 - Ecological Society of America Annual Meeting PB - ESA CY - Fort Lauderdale, Florida, USA N1 - [Original String]:Morrissey, E.M., Mau, R.L., Schwartz, E., Caporaso, J.G., Dijkstra, P., McHugh, T., Marks, J.C., Price, L.B., Liu, C.M. and Hungate, B.A. (2016). Taxon-specific microbial activities explain soil carbon cycling dynamics. ESA August 7-12, Fort Lauderdale. ER - TY - CONF T1 - Taxon-Specific Responses To Whole System Carbon Cycling In The Root Microbiome. T2 - Phytobiomes from microbes to plant ecosystems Y1 - 2016 A1 - P Dijkstra A1 - RL Mau A1 - McHugh,TA A1 - BJ Koch A1 - Marks,JC A1 - van Groenigen,K-J A1 - Liu,X-J A1 - Schwartz,E A1 - Morrissey,EM A1 - Hungate,BA AB -

Dijkstra, P., Mau, R.L., McHugh, T.A., Koch, B.J., Marks, J.C., vanGroenigen, K-J., Liu, X-J. A., Schwartz, E., Morrissey, E.M. and Hungate, B.A. (2016). From Taxon-Specific Responses To Whole System Carbon Cycling In The Root Microbiome. Phytobiomes: from microbes to plant ecosystems. Nov 2016, .

JF - Phytobiomes from microbes to plant ecosystems T3 - Phytobiomes from microbes to plant ecosystems CY - Santa Fe, New Mexicao, USA N1 - [Original String]:Dijkstra, P., Mau, R.L., McHugh, T.A., Koch, B.J., Marks, J.C., van Groenigen, K-J., Liu, X-J. A., Schwartz, E., Morrissey, E.M. and Hungate, B.A. (2016). From Taxon-Specific Responses To Whole System Carbon Cycling In The Root Microbiome. Phytobiomes: from microbes to plant ecosystems. Nov 2016, Santa Fe NM. ER - TY - JOUR T1 - Temperature is better than precipitation as a predictor of plant community assembly across a dryland region. JF - Journal of Vegetation Science Y1 - 2016 A1 - Butterfield,BJ A1 - Munson,SM AB -

Question

How closely do plant communities track climate? Research suggests that plant species converge toward similar environmental tolerances relative to the environments that they experience. Whether these patterns apply to severe environments or scale up to plant community-level patterns of relative climatic tolerances is poorly understood. Using estimates of species' climatic tolerances acquired from occurrence records, we determined the contributions of individual species' climatic niche breadths and environmental filtering to the relationships between community-average climatic tolerances and the local climates experienced by those communities.

Location

Southwestern United States drylands.

Methods

Interspecific variation in niche breadth was assessed as a function of species' climatic optima (median climatic niche value). The relationships between climatic optima and tolerances were used as null expectations for the relationship between abundance-weighted mean climatic tolerances of communities and the local climate of that community. Deviations from this null expectation indicate that species with greater or lesser climatic tolerances are favoured relative to co-occurring species. The intensity of environmental filtering was estimated by comparing the range of climatic tolerances within each community to a null distribution generated from a random assembly algorithm.

Results

The temperature niches of species were consistently symmetrical and of similar breadths, regardless of their temperature optima. In contrast, precipitation niches were skewed toward wetter conditions, and niche breadth increased with increasing precipitation optima. At the community level, relationships with climate were much stronger for temperature than for precipitation. Furthermore, cold and heat were stronger assembly filters than drought or precipitation, with the intensity of environmental filtering increasing at both ends of climatic gradients. Community-average climatic tolerances did deviate significantly from null expectations, indicating that species with higher or lower relative climatic tolerances were favoured under certain conditions.

Conclusions

Despite strong water limitation of plant performance in dryland ecosystems, communities tracked variation in temperature much more closely, intimating strong responses to anticipated temperature increases. Furthermore, abundance distributions were biased toward species with higher or lower relative climatic tolerances under different climatic conditions, but predictably so, indicating the need for assembly models that include processes other than simple environmental filtering.

VL - 27 IS - 5 N1 - [Original String]:Butterfield, B.J. and Munson, S.M. (In press). Temperature is better than precipitation as a predictor of plant community assembly across a dryland region. Journal of Vegetation Science. ER - TY - JOUR T1 - Tree genotype influences ectomycorrhizal fungal community structure: Ecological and evolutionary implications JF - FUNGAL ECOLOGY Y1 - 2016 A1 - Lamit,LJ A1 - LM Holeski A1 - L Flores-Renteria A1 - TG Whitham A1 - CA Gehring AB - Although the eco-evolutionary dynamics of multicellular organisms are intertwined with the microorganisms that colonize them, there is only a rudimentary understanding of how a host's genotype influences its microbiome. We utilize Populus angustifolia to test whether communities of essential symbionts, ectomycorrhizal fungi (EMF), vary among host genotypes. Further, we test whether EMF communities covary among tree genotypes with the chemistry of senescent leaves and aboveground biomass, traits important to tree fitness, and carbon and nutrient cycling. We found: 1) EMF composition, colonization and the Basidiomycota to Ascomycota ratio varied among tree genotypes (broad-sense heritability=0.10鈥0.25). 2) EMF composition did not covary among genotypes with aboveground biomass but it did covary with senescent leaf chemistry ( rho =0.29), primarily due to a single genotype. These findings demonstrate a link between tree genotype and EMF communities, which has implications for fungal diversity, host-symbiont interactions and aboveground-belowground linkages in ecological and evolutionary contexts. VL - 24 UR - http://www.sciencedirect.com/science/article/pii/S1754504816300563 ER - TY - JOUR T1 - Tree genotype influences ectomycorrhizal fungal community structure: ecological and evolutionary implications. JF - Fungal Ecology Y1 - 2016 A1 - L.J. Lamit A1 - L. M. Holeski A1 - L. Flores-Rentería A1 - T. G. Whitham A1 - C. A. Gehring KW - Ectomycorrhizal fungi KW - Genotype Heritability KW - Populus KW - Senescent leaf chemistry AB -

Although the eco-evolutionary dynamics of multicellular organisms are intertwined with the microorganisms that colonize them, there is only a rudimentary understanding of how a host's genotype influences its microbiome. We utilize Populus angustifolia to test whether communities of essential symbionts, ectomycorrhizal fungi (EMF), vary among host genotypes. Further, we test whether EMF communities covary among tree genotypes with the chemistry of senescent leaves and aboveground biomass, traits important to tree fitness, and carbon and nutrient cycling. We found: 1) EMF composition, colonization and the Basidiomycota to Ascomycota ratio varied among tree genotypes (broad-sense heritability = 0.10–0.25). 2) EMF composition did not covary among genotypes with aboveground biomass but it did covary with senescent leaf chemistry (rho = 0.29), primarily due to a single genotype. These findings demonstrate a link between tree genotype and EMF communities, which has implications for fungal diversity, host-symbiont interactions and aboveground-belowground linkages in ecological and evolutionary contexts.

VL - 24 UR - https://www.sciencedirect.com/science/article/pii/S1754504816300563 IS - Part B ER - TY - CONF T1 - Towards Intelligent Closed-Loop Workflows for Ecological Research Dynamic Data-driven Environmental Systems T2 - Dynamic Data-driven Environmental Systems Science Conference (DyDESS) Y1 - 2014 A1 - Knapp,J A1 - Elo,M A1 - Schaffer,J A1 - PG Flikkema JF - Dynamic Data-driven Environmental Systems Science Conference (DyDESS) T3 - Dynamic Data-driven Environmental Systems Science Conference (DyDESS) PB - DyDESS CY - Cambridge, MA, USA VL - 2014 N1 - [Original String]:Knapp, J.D., M. Elo, J. Shaeffer, and P.G. Flikkema. 2014. Towards Intelligent Closed-Loop Workflows for Ecological Research. Dynamic Data-driven Environmental Systems Science Conference (DyDESS), November 5-7, 2014, Cambridge, MA. ER - TY - CONF T1 - Towards Cyber-Eco Systems: Networked Sensing, Inference and Control for Distributed Ecological Experiments T2 - IEEE International Conference on Cyber, Physical and Social Computing Y1 - 2012 A1 - PG Flikkema A1 - Yamamoto,KR A1 - Boegli,S A1 - Porter,C A1 - PL Heinrich JF - IEEE International Conference on Cyber, Physical and Social Computing T3 - IEEE International Conference on Cyber, Physical and Social Computing ER - TY - JOUR T1 - Tree hybridization and genotypic variation drive cryptic speciation of a specialist mite herbivore. JF - Evolution; international journal of organic evolution Y1 - 2008 A1 - Evans,Luke M A1 - Allan,Gerard J A1 - Shuster,Stephen M A1 - Woolbright,Scott A A1 - Whitham,Thomas G KW - Analysis of Variance KW - Animals KW - Base Sequence KW - Cluster Analysis KW - Crosses, Genetic KW - DNA Primers KW - Genetic Variation KW - Genetics, Population KW - Geography KW - Host-Parasite Interactions KW - Hybridization, Genetic KW - Mites KW - Molecular Sequence Data KW - Phylogeny KW - Populus KW - Sequence Analysis, DNA KW - Utah AB -

Few studies have investigated the roles that plant hybridization and individual plant genotype play in promoting population divergence within arthropod species. Using nrDNA sequence information and reciprocal transfer experiments, we examined how tree cross type (i.e., pure Populus angustifolia and P. angustifolia x P. fremontii F(1) type hybrids) and individual tree genotype influence host race formation in the bud-galling mite Aceria parapopuli. Three main findings emerged: (1) Strong genetic differentiation of mite populations found on pure P. angustifolia and F(1) type hybrids indicates that these mites represent morphologically cryptic species. (2) Within the F(1) type hybrids, population genetic analyses indicate migration among individual trees; however, (3) transfer experiments show that the mites found on heavily infested F(1) type trees perform best on their natal host genotype, suggesting that genetic interactions between mites and their host trees drive population structure, local adaptation, and host race formation. These findings argue that hybridization and genotypic differences in foundation tree species may drive herbivore population structure, and have evolutionary consequences for dependent arthropod species.

VL - 62 SN - 0014-3820 UR - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=18752612&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumhttp://www.ncbi. IS - 12 ER - TY - JOUR T1 - Terrestrial transects for global change research JF - Vegetation Y1 - 1995 A1 - GW Koch A1 - Vitousek,PM A1 - Steffen,WL A1 - Walker,BH AB - The International Geosphere-Biosphere Program has proposed a set of large-scale terrestrial transects to study the effects of changes in climate, land use, and atmospheric composition (“global change”) on biogeochemistry, surface-atmosphere exchange, and vegetation dynamics of terrestrial ecosystems. The transects (≈ 1000 km) will be located along existing environmental and land use intensity gradients that span transitions between biomes in regions likely to be widely affected by forcing from components of global change or where the impacts of global change are likely to feed back to affect atmospheric, climatic, or hydrologic systems. Experimental studies on the transects will examine short-term changes in ecosystem function and biosphere-atmosphere interaction in response to variation in primary controlling variables. A hierarchy of modeling approaches will develop predictions of long-term changes in biome boundaries and vegetation distribution. The proposed initial set of IGBP terrestrial transects are located in four key regions: (1) humid tropical forests undergoing land use change, (2) high latitudes including the transition from boreal forest to tundra, (3) semi-arid tropical regions including transitions from dry forest to shrublands and savannas, and (4) mid latitude semi-arid regions encompassing transitions from shrubland or grassland to forests. We discuss here the rationale and general research design of transect studies proposed for each of these priority regions. VL - 121 UR - http://link.springer.com/article/10.1007/BF00044672 ER -