In a previous paper, we developed an analytical clumped two-stream model (ACTS) of canopy radiative transfer from an analytical geometric-optical and radiative transfer (GORT) scheme (Ni-Meister et al., 2010). The ACTS model accounts for clumping of foliage and the influence of trunks in vegetation canopies for modeling of photosynthesis, radiative fluxes and surface albedo in dynamic global vegetation models (DGVMs), and particularly for the Ent Dynamic Global Terrestrial Ecosystem Model (DGTEM). This study evaluates the gap probability and transmittance estimates from the ACTS model by comparing the modeled results with ground-based data, as well as with the original full GORT model and a layered Beer’s law scheme. The ground data used in this study include vertical profile measurements of incident photosynthetically active radiation (PAR) in (1) mixed deciduous forests in Morgan-Monroe State Forest, IN, USA, (2) coniferous forests in central Canada, (3) mixed deciduous forests in Harvard Forest, MA, and (4) ground lidar measurements of the canopy gap fraction in woodland in Australia.
This study develops a simple but physically based canopy radiative transfer scheme for photosynthesis, radiative fluxes and surface albedo estimates in dynamic global vegetation models (DGVMs), and particularly for the Ent Dynamic Global Terrestrial Ecosystem Model (Ent DGTEM). The Ent DGTEM can represent vegetation in mixed as opposed to homogeneous canopies. With active growth and competition, it must predict radiative transfer for dynamically changing vegetation structure, and requires computational speed for coupling with atmospheric general circulation models (GCMs). The canopy radiative transfer scheme accounts for both vertical and horizontal heterogeneity of plant canopies by combining the simple two-stream scheme with a well-described actual vertical foliage profile, an analytically derived foliage clumping factor from geometric optical theory, and, for needleleaf trees, an empirical needle-to-shoot-clumping factor. In addition, the model accounts for the effect of trunks, which is significant in bare canopies. This model provides better radiation estimates (light profiles, albedo) than the two-stream scheme currently being used in most GCMs to describe light interactions with vegetation canopies. This scheme has the same computational cost as the current typical scheme being used in GCMs, but promises to provide better canopy radiative transfer estimates for DGVMs, particularly those that model heterogeneous vegetation canopies.
Aggregates of archaea and sulfate-reducing bacteria (SRB) recently discovered in methane-seep sediments are widely assumed to engage in anaerobic methane oxidation (AMO), but the reaction mechanism remains poorly understood. We used a spherical diffusion-reaction model that incorporates thermodynamic controls, realistic aggregate morphology, and essential elements of cell structure to quantify maximum reaction rates and energy yields for competing mechanisms, to determine how cellular energy yields are affected by aggregate size and morphology, and to investigate the impact of organic-matter remineralization on archaea and SRB in the aggregate.
Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox‐dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.
There is increasing evidence for the existence of unique ecosystems that are dominated by locally adapted microbiota which harbour distinct lineages and biological capabilities, much like the macrobiota of Darwin’s Galapagos Islands. As a primary example of such a system, we highlight key discoveries from the Cuatro Ciénegas basin in Mexico. We argue that high microbial endemism requires a combination of geographical isolation, long-term continuity and mechanisms for reducing the intensity of horizontal gene transfer (HGT). We also propose that strong phosphorus limitation has an important role in microbial diversification by reducing the intensity of HGT.
On other worlds, plants could be red, blue, even black
Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes)1,2,3,4. Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.
Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes)1,2,3,4. Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted.
Habitability can be formulated as a balance between the biological demand for energy and the corresponding potential for meeting that demand by transduction of energy from the environment into biological process. The biological demand for energy is manifest in two requirements, analogous to the voltage and power requirements of an electrical device, which must both be met if life is to be supported. These requirements exhibit discrete (non-zero) minima whose magnitude is set by the biochemistry in question, and they are increased in quantifiable fashion by (i) deviations from biochemically optimal physical and chemical conditions and (ii) energy-expending solutions to problems of resource limitation. The possible rate of energy transduction is constrained by (i) the availability of usable free energy sources in the environment, (ii) limitations on transport of those sources into the cell, (iii) upper limits on the rate at which energy can be stored, transported, and subsequently liberated by biochemical mechanisms (e.g., enzyme saturation effects), and (iv) upper limits imposed by an inability to use “power” and “voltage” at levels that cause material breakdown. A system is habitable when the realized rate of energy transduction equals or exceeds the biological demand for energy. For systems in which water availability is considered a key aspect of habitability (e.g., Mars), the energy balance construct imposes additional, quantitative constraints that may help to prioritize targets in search-for-life missions. Because the biological need for energy is universal, the energy balance construct also helps to constrain habitability in systems (e.g., those envisioned to use solvents other than water) for which little constraint currently exists.
One of the key biochemical developments during the evolution of life was the invention of the oxygen-evolving complex (OEC) of photosystem II, responsible for catalyzing the oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. Though there have been a number of recent, key advances towards understanding how this remarkable chemistry is carried out, it remains a fundamental mystery how this complicated, four electron transfer process originated. Here we review some of these advances and resulting hypotheses on the origin and early evolution of the OEC. In addition, we present evidence suggesting that the four manganese-containing core of the OEC shares structural homology at the atomic level with the active sites of several distinct two manganese-containing enzymes, including manganese catalase, which carries out the oxidation of hydrogen peroxide. We discuss the implications for the plausible origin of oxygenic photosynthesis.
Why do plants reflect in the green and have a “red edge” in the red, and should extrasolar photosynthesis be the same? We provide (1) a brief review of how photosynthesis works, (2) an overview of the diversity of photosynthetic organisms, their light harvesting systems, and environmental ranges, (3) a synthesis of photosynthetic surface spectral signatures, and (4) evolutionary rationales for photosynthetic surface reflectance spectra with regard to utilization of photon energy and the planetary light environment. We found the “near-infrared (NIR) end” of the red edge to trend from blue-shifted to reddest for (in order) snow algae, temperate algae, lichens, mosses, aquatic plants, and finally terrestrial vascular plants. The red edge is weak or sloping in lichens. Purple bacteria exhibit possibly a sloping edge in the NIR. More studies are needed on pigment–protein complexes, membrane composition, and measurements of bacteria before firm conclusions can be drawn about the role of the NIR reflectance. Pigment absorbance features are strongly correlated with features of atmospheric spectral transmittance: P680 in Photosystem II with the peak surface incident photon flux density at ∼685 nm, just before an oxygen band at 687.5 nm; the NIR end of the red edge with water absorbance bands and the oxygen A-band at 761 nm; and bacteriochlorophyll reaction center wavelengths with local maxima in atmospheric and water transmittance spectra. Given the surface incident photon flux density spectrum and resonance transfer in light harvesting, we propose some rules with regard to where photosynthetic pigments will peak in absorbance: (1) the wavelength of peak incident photon flux; (2) the longest available wavelength for core antenna or reaction center pigments; and (3) the shortest wavelengths within an atmospheric window for accessory pigments. That plants absorb less green light may not be an inefficient legacy of evolutionary history, but may actually satisfy the above criteria.
As photosynthesis on Earth produces the primary signatures of life that can be detected astronomically at the global scale, a strong focus of the search for extrasolar life will be photosynthesis, particularly photosynthesis that has evolved with a different parent star. We take previously simulated planetary atmospheric compositions for Earth-like planets around observed F2V and K2V, modeled M1V and M5V stars, and around the active M4.5V star AD Leo; our scenarios use Earth’s atmospheric composition as well as very low O2 content in case anoxygenic photosynthesis dominates. With a line-by-line radiative transfer model, we calculate the incident spectral photon flux densities at the surface of the planet and under water. We identify bands of available photosynthetically relevant radiation and find that photosynthetic pigments on planets around F2V stars may peak in absorbance in the blue, K2V in the red-orange, and M stars in the near-infrared, in bands at 0.93–1.1 μm, 1.1–1.4 μm, 1.5–1.8 μ m, and 1.8–2.5 μm.
A coupled photochemical‐ecosystem model has been developed to simulate the early Archean biosphere. The model incorporates kinetic and nutrient limitations on biological productivity, along with constraints imposed by metabolic thermodynamics. We have used this model to predict the biogenic CH4 flux and net primary productivity (NPP) of the marine biosphere prior to the advent of oxygenic photosynthesis. Organisms considered include chemotrophic and organotrophic methanogens, H2‐, H2S‐, and Fe‐using anoxygenic phototrophs, S‐reducing bacteria, CO‐using acetogens, and fermentative bacteria.