Christopher K. Algar

Gene-centric approach to integrating environmental genomics and biogeochemical models

Significance Modern molecular tools provide an invaluable window into the marine microbial world by identifying organisms and their metabolisms through the analysis of genetic material. Microbial communities are ubiquitous throughout the oceans and exert great influence over ocean chemistry, yet they are rarely included explicitly in models of marine biogeochemistry, such as those used to predict the response of the oceans to environmental problems (e.g., climate change). Here, we present a unique way of integrating genetic data from state-of-the-art molecular tools into biogeochemical models to improve their predictive power, better constrain geochemical processes—especially those that are not apparent from chemical measurements—and gain a deeper insight into ocean chemistry and microbiology. Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth’s biogeochemistry.

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise.

Summary Warm fluids emanating from hydrothermal vents can be used as windows into the rocky subseafloor habitat and its resident microbial community. Two new vent systems on the Mid‐Cayman Rise each exhibits novel geologic settings and distinctively hydrogen‐rich vent fluid compositions. We have determined and compared the chemistry, potential energy yielding reactions, abundance, community composition, diversity, and function of microbes in venting fluids from both sites: Piccard, the worlds deepest vent site, hosted in mafic rocks; and Von Damm, an adjacent, ultramafic‐influenced system. Von Damm hosted a wider diversity of lineages and metabolisms in comparison to Piccard, consistent with thermodynamic models that predict more numerous energy sources at ultramafic systems. There was little overlap in the phylotypes found at each site, although similar and dominant hydrogen‐utilizing genera were present at both. Despite the differences in community structure, depth, geology, and fluid chemistry, energetic modelling and metagenomic analysis indicate near functional equivalence between Von Damm and Piccard, likely driven by the high hydrogen concentrations and elevated temperatures at both sites. Results are compared with hydrothermal sites worldwide to provide a global perspective on the distinctiveness of these newly discovered sites and the interplay among rocks, fluid composition and life in the subseafloor.

The Thermodynamics of Marine Biogeochemical Cycles: Lotka Revisited

Nearly 100 years ago, Alfred Lotka published two short but insightful papers describing how ecosystems may organize. Principally, Lotka argued that ecosystems will grow in size and that their cycles will spin faster via predation and nutrient recycling so as to capture all available energy, and that evolution and natural selection are the mechanisms by which this occurs and progresses. Lotkas ideas have often been associated with the maximum power principle, but they are more consistent with recent developments in nonequilibrium thermodynamics, which assert that complex systems will organize toward maximum entropy production (MEP). In this review, we explore Lotkas hypothesis within the context of the MEP principle, as well as how this principle can be used to improve marine biogeochemistry models. We need to develop the equivalent of a climate model, as opposed to a weather model, to understand marine biogeochemistry on longer timescales, and adoption of the MEP principle can help create such models.

Use of Receding Horizon Optimal Control to Solve MaxEP-Based Biogeochemistry Problems

The maximum entropy production (MaxEP) principle has been applied to steady state systems, but biogeochemical problems of interest are typically transient in nature. To apply MaxEP to biogeochemical reaction networks, we propose that living systems maximum entropy production over appropriate time horizons based on strategic information stored in their genomes, which differentiates them from inanimate chemistry, such as fire, that maximizes entropy production instantaneously. We develop a receding horizon optimal control procedure that maximizes internal entropy production over different intervals of time. This procedure involves optimizing the stoichiometry of a reaction network to determine how biological structure is partitioned to reactions over an interval of time. The modeling work is compared to a methanotrophic microcosm experiment that is being conducted to examine how microbial systems integrate entropy production over time when subject to time varying energy input attained by periodically cycling feed-gas composition. The MaxEP-based model agrees well with experimental results, and model analysis shows that increasing the optimization time horizon increases internal entropy production.

THE MECHANICS OF SOFT COHESIVE SEDIMENTS DURING EARLY DIAGENESIS

Natural, surficial, cohesive (clay-bearing), aquatic sediments are subject to a variety of phenomena in which physics, rather than say chemistry, plays an essential role; this includes, but is not limited to, bioturbation, self-weight compaction, and phase growth. Scientific monographs (e.g., Berner, 1971, 1980; Boudreau, 1997; DiToro, 2001; Burdige, 2006; Schultz and Zabel, 2006) that focus on early diagenesis, i.e., those changes occurring in the top 1–10 meters (m) of aqueous sediments, make only passing reference to the physics of early diagenetic phenomena. In contrast, civil engineers, soil physicists and geophysicists have afforded great attention to the physics/mechanics of compaction, particularly in soils, anthropogenic sediments and basin-scale studies (e.g., Yong and Warkentin, 1966; Giles, 1997; Wang, 2000; Craig, 2004; Mitchell and Soga, 2005; Das, 2008); yet, this knowledge has not been effectively transferred to obtain a better understanding of early diagenesis.