Ecological modelling approaches for predicting emergent properties in microbial communities

NI van den Berg, D Machado, S Santos… - Nature ecology & …, 2022 - nature.com
Recent studies have brought forward the critical role of emergent properties in sha**
microbial communities and the ecosystems of which they are a part. Emergent properties …

Trait-based modelling in ecology: a review of two decades of research

L Zakharova, KM Meyer, M Seifan - Ecological Modelling, 2019 - Elsevier
Trait-based approaches are an alternative to species-based approaches for functionally
linking individual organisms with community structure and dynamics. In the trait-based …

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

G Wang, Q Gao, Y Yang, SE Hobbie… - Global change …, 2022 - Wiley Online Library
Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental
changes have received increasing attention. However, large uncertainties in model …

Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean

A Srivastava, DEM Saavedra, B Thomson… - The ISME …, 2021 - academic.oup.com
Alkaline phosphatase (APase) is one of the marine enzymes used by oceanic microbes to
obtain inorganic phosphorus (Pi) from dissolved organic phosphorus to overcome P …

Climate and edaphic factors drive soil enzyme activity dynamics and tolerance to Cd toxicity after rewetting of dry soil

X Tan, J He, Y Nie, X Ni, Q Ye, L Ma… - Science of The Total …, 2023 - Elsevier
The intense drying-rewetting cycle due to climate change can affect soil microbial
community composition and function, resulting in long-term consequences for belowground …

Drought conditions maximize the impact of high‐frequency flow variations on thermal regimes and biogeochemical function in the hyporheic zone

X Song, X Chen, J Stegen, G Hammond… - Water Resources …, 2018 - Wiley Online Library
Anthropogenic activities, especially dam operations, often induce larger and more frequent
stage fluctuations than those occurring in natural rivers. However, long‐term impacts of such …

Transcriptional and environmental control of bacterial denitrification and N2O emissions

H Gaimster, M Alston, DJ Richardson… - FEMS microbiology …, 2018 - academic.oup.com
In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent
respiration to nitrate (NO3−) respiration in which the NO3− is sequentially reduced via nitrite …

Exploring the determinants of organic matter bioavailability through substrate-explicit thermodynamic modeling

F Ahamed, Y You, A Burgin, JC Stegen… - Frontiers in …, 2023 - frontiersin.org
Microbial decomposition of organic matter (OM) in river corridors is a major driver of nutrient
and energy cycles in natural ecosystems. Recent advances in omics technologies enabled …

Representing organic matter thermodynamics in biogeochemical reactions via substrate-explicit modeling

HS Song, JC Stegen, EB Graham, JY Lee… - Frontiers in …, 2020 - frontiersin.org
Predictive biogeochemical modeling requires data-model integration that enables explicit
representation of the sophisticated roles of microbial processes that transform substrates …

Reactive transport modeling of microbial dynamics

C Meile, TD Scheibe - Elements: An International …, 2019 - pubs.geoscienceworld.org
Reactive transport modeling of microbially mediated processes has contributed significantly
to an improved understanding of elemental cycling in Earth's near-surface environments. We …