scholarly journals Understanding microbiomes through trait-based ecology

2018 ◽  
Vol 39 (1) ◽  
pp. 53
Author(s):  
Jennifer L Wood ◽  
Ashley E Franks

Ecology is the study of the interactions amongst organisms and their environment1. In microbial ecology, a major goal is to understand how environmental microbiomes impact ecosystem health and function. This desire to mechanistically link micro and macro processes is increasingly highlighting the importance of functional ecology, which aims to develop an understanding of relationships using functional traits, as opposed to species names. A functional trait may be any morphological or physiological trait that influences the performance or fitness of an individual in a given environment, such as regeneration time, size, antibiotic production or motility2. Although it is not possible to measure a given trait for each individual within an environmental microbiome, community-level functional traits can be derived from the community metagenome either directly via shotgun sequencing or predictively (for bacteria) from 16S rRNA profiles3. In understanding environmental microbiomes, functional traits have unique properties that can be utilised to (1) compare microbiomes using an ecological framework, (2) understand processes governing community assembly, and (3) build predictive ecological models.

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Anne-Christine Monnet ◽  
Kévin Cilleros ◽  
Frédéric Médail ◽  
Marwan Cheikh Albassatneh ◽  
Juan Arroyo ◽  
...  

AbstractTrees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.


2020 ◽  
Vol 51 (1) ◽  
pp. 533-560 ◽  
Author(s):  
Joseph A. Tobias ◽  
Jente Ottenburghs ◽  
Alex L. Pigot

The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.


2021 ◽  
Vol 9 (4) ◽  
pp. 766
Author(s):  
Christopher J. Ellis ◽  
Johan Asplund ◽  
Renato Benesperi ◽  
Cristina Branquinho ◽  
Luca Di Nuzzo ◽  
...  

Community ecology has experienced a major transition, from a focus on patterns in taxonomic composition, to revealing the processes underlying community assembly through the analysis of species functional traits. The power of the functional trait approach is its generality, predictive capacity such as with respect to environmental change, and, through linkage of response and effect traits, the synthesis of community assembly with ecosystem function and services. Lichens are a potentially rich source of information about how traits govern community structure and function, thereby creating opportunity to better integrate lichens into ‘mainstream’ ecological studies, while lichen ecology and conservation can also benefit from using the trait approach as an investigative tool. This paper brings together a range of author perspectives to review the use of traits in lichenology, particularly with respect to European ecosystems from the Mediterranean to the Arctic-Alpine. It emphasizes the types of traits that lichenologists have used in their studies, both response and effect, the bundling of traits towards the evolution of life-history strategies, and the critical importance of scale (both spatial and temporal) in functional trait ecology.


2001 ◽  
Vol 17 (suppl) ◽  
pp. S69-S75 ◽  
Author(s):  
N. Ole Nielsen

The promotion of human health must be embedded in the wider pursuit of ecosystem health. Interventions will be impaired if ecosystem-linked determinants of health are not taken into account. In the extreme case, if ecosystems lose their capacity for renewal, society will lose life support services. Essential features of ecosystem health are the capacity to maintain integrity and to achieve reasonable and sustainable human goals. An ecosystem approach to research and management must be transdisciplinary and assure participation of stakeholders. These requisites provide a means for science to better deal with the complexity of ecosystems, and for policy-makers and managers to establish and achieve reasonable societal goals. The ecosystem approach can determine links between human health and activities or events which disturb ecosystem state and function. Examples are: landscape disturbance in agriculture, mining, forestry, urbanization, and natural disasters. An understanding of these links can provide guidance for management interventions and policy options that promote human health. An ecosystem approach to management must be adaptive because of irreducible uncertainty in ecosystem function.


2021 ◽  
Vol 12 ◽  
Author(s):  
Caishuang Huang ◽  
Yue Xu ◽  
Runguo Zang

Understanding how environmental change alters the composition of plant assemblages is a major challenge in the face of global climate change. Researches accounting for site-specific trait values within forest communities help bridge plant economics theory and functional biogeography to better evaluate and predict relationships between environment and ecosystem functioning. Here, by measuring six functional traits (specific leaf area, leaf dry matter content, leaf nitrogen, and phosphorus concentration, leaf nitrogen/phosphorus, wood density) for 292 woody plant species (48,680 individuals) from 250 established permanent forest dynamics plots in five locations across the subtropical evergreen broadleaved forests (SEBLF) in China, we quantified functional compositions of communities by calculating four trait moments, i.e., community-weighted mean, variance, skewness, and kurtosis. The geographical (latitudinal, longitudinal, and elevational) patterns of functional trait moments and their environmental drivers were examined. Results showed that functional trait moments shifted significantly along the geographical gradients, and trait moments varied in different ways across different gradients. Plants generally showed coordinated trait shifts toward more conservative growth strategies (lower specific leaf area, leaf N and P concentration while higher leaf nitrogen/phosphorus and wood density) along increasing latitude and longitude. However, trends opposite to the latitudinal and longitudinal patterns appeared in trait mean values along elevation. The three sets of environmental variables (climate, soil and topography) explained 35.0–69.0%, 21.0–56.0%, 14.0–31.0%, and 16.0–30.0% of the variations in mean, variance, skewness, and kurtosis across the six functional traits, respectively. Patterns of shifts in functional trait moments along geographical gradients in the subtropical region were mainly determined by the joint effects of climatic and edaphic conditions. Climate regimes, especially climate variability, were the strongest driving force, followed by soil nutrients, while topography played the least role. Moreover, the relationship of variance, skewness and kurtosis with climate and their geographical patterns suggested that rare phenotypes at edges of trait space were selected in harsher environments. Our study suggested that environmental filtering (especially climate variability) was the dominant process of functional assembly for forest communities in the subtropical region along geographical gradients.


2014 ◽  
Vol 328 ◽  
pp. 1-9 ◽  
Author(s):  
Matthew B. Russell ◽  
Christopher W. Woodall ◽  
Anthony W. D’Amato ◽  
Grant M. Domke ◽  
Sassan S. Saatchi

2021 ◽  
Author(s):  
Carlos Aguilar-Trigueros ◽  
Mark Fricker ◽  
Matthias Rillig

<p>Fungal mycelia consist of an interconnected network of filamentous hyphae and represent the dominant phase of the lifecycle in all major fungal phyla, from basal to more recent clades. Indeed, the ecological success of fungi on land is partly due to such filamentous network growth. Nevertheless, fungal ecologists rarely use network features as functional traits. Given the widespread occurrence of this body type, we hypothesized that interspecific variation in network features may reflect both phylogenetic affiliation and distinct ecological strategies among species. We show first that there is high interspecific variation in network parameters of fungi, which partly correlates with taxonomy; and second that network parameters, related to predicted-mycelial transport mechanisms during the exploration phase, reveal the trait space in mycelium architecture across species.  This space predicts a continuum of ecological strategies along two extremes: from highly connected mycelia with high resilience to damage but limited transport efficiency, to poorly connected mycelia with low resilience but high transport efficiency. We argue that mycelial networks are potentially a rich source of information to inform functional trait analysis in fungi, but we also note the challenges in establishing common principles and processing pipelines that are required to facilitate widespread use of network properties as functional traits in fungal ecology.</p>


2019 ◽  
Vol 41 (1) ◽  
pp. 83
Author(s):  
Na Zhao ◽  
Xinqing Shao ◽  
Chao Chen ◽  
Jiangwen Fan ◽  
Kun Wang

Plant biomass is the most fundamental component of ecosystems. The spatial stability of plant biomass is important, and the mechanisms regulating plant biomass spatial variability in variable environments are a central focus of ecology. However, they have rarely been explored. We conducted an experiment to test how diversity and functional traits affected variation in biomass and community response to nutrient availability in three plant communities: natural; forb, legume, and bunchgrass; and rhizomatous grass. We found that biomass stability rarely changed with increasing taxonomic species richness and functional group richness but declined with increasing Shannon–Weiner indices (the combination of richness and evenness) and functional trait diversity. However, differences in plant species composition generated different responses in both the amount and spatial variation of biomass following nutrient addition. Because rhizomatous grasses are weakly competitive in nutrient-poor conditions, interaction between resource-acquisitive (grass) and stress-tolerant (forb) species in the natural community conferred the greatest overall stability. The rapid nutrient acquisition ability of the rhizomatous grass Leymus chinensis was stimulated in nutrient-abundant conditions. The functional traits of this dominant species overrode the diversity interaction effects of the natural and forb, legume, and bunchgrass communities. This ultimately resulted in the rhizomatous grass community being the most stable. Community stability was strongly determined by a few key species, particularly rhizomatous grasses, rather than by the average response of all species, thereby supporting the mass ratio hypothesis. Our results indicated that rhizomatous grasses could provide vegetative productivity to reduce soil loss and prevent degradation of L. chinensis-dominant grassland. Thus, protecting specific species is critical for maintaining rangeland ecosystem functions. Moreover, the conservation importance of grasses, non-leguminous forbs, legumes, or even rare species could not be ignored. Maintaining stability mechanisms in natural grasslands is complex, and therefore, further studies need to focus on finding a unified mechanism that can regulate appreciable biomass variation under shifting environmental conditions.


Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1733
Author(s):  
Livia Paleari ◽  
Fosco M. Vesely ◽  
Riccardo A. Ravasi ◽  
Ermes Movedi ◽  
Sofia Tartarini ◽  
...  

Cultivar recommendation is a key factor in cropping system management. Classical approaches based on comparative multi-environmental trials can hardly explore the agro-climatic and management heterogeneity farmers may have to face. Moreover, they struggle to keep up with the number of genotypes commercially released each year. We propose a new approach based on the integration of in silico ideotyping and functional trait profiling, with the common bean (Phaseoulus vulgaris L.) in Northern Italy as a case study. Statistical distributions for six functional traits (light extinction coefficient, radiation use efficiency, thermal time to first pod and maturity, seed weight, plant height) were derived for 24 bean varieties. The analysis of soil, climate and management in the study area led us to define 21 homogeneous contexts, for which ideotypes were identified using the crop model STICS (Simulateur mulTIdisciplinaire pour les Cultures Standard), the E-FAST (Extended Fourier Amplitude Sensitivity Test) sensitivity analysis method, and the distributions of functional traits. For each context, the 24 cultivars were ranked according to the similarity (weighted Euclidean distance) with the ideotype. Context-specific ideotypes mainly differed for phenological adaptation to specific combinations of climate and management (sowing time) factors, and this reflected in the cultivar recommendation for the different contexts. Feedbacks from bean technicians in the study area confirmed the reliability of the results and, in turn, of the proposed methodology.


2019 ◽  
Vol 70 (11) ◽  
pp. 1611 ◽  
Author(s):  
Xiaoyun Bai ◽  
Congcong Guo ◽  
Mamun Abdullah Al ◽  
Alan Warren ◽  
Henglong Xu

Multifunctional trait analysis is increasingly recognised as an effective tool for assessing ecosystem function and environmental quality. Here, a baseline study was performed at four depths (i.e. 1, 2, 3.5 and 5m) in Yellow Sea coastal waters of northern China in order to determine the optimal depth for bioassessment using biological traits of biofilm-dwelling ciliates. Community-weighted means (CWM) from functional traits system were used to summarise the trait distribution and functional diversity of ciliates among the four depths during a 1-month colonisation period. Functional trait distribution revealed a clear temporal variation among the four depths. In total, 3 of 17 functional traits (i.e. feeding type, body size and flexibility) showed significant temporal patterns. Bootstrapped averaging and permutational multivariate analysis of variance (PERMANOVA) tests demonstrated that the colonisation pattern of biofilm-dwelling ciliates as expressed by CWM at 1 and 2m differed significantly from those at 3.5 and 5m. Functional diversity indices showed lower variability at 1 and 2m than at 3.5 and 5m. These results suggest that 1 and 2m are the preferred sampling depths for bioassessment of marine water quality using biological traits of biofilm-dwelling ciliates.


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