Phototrophic Species Research Articles

Evolution of Thylakoid Structural Diversity.

Oxygenic photosynthesis evolved billions of years ago, becoming Earth's main source of biologically available carbon and atmospheric oxygen. Since then, phototrophic organisms have diversified from prokaryotic cyanobacteria into several distinct clades of eukaryotic algae and plants through endosymbiosis events. This diversity can be seen in the thylakoid membranes, complex networks of lipids, proteins, and pigments that perform the light-dependent reactions of photosynthesis. In this review, we highlight the structural diversity of thylakoids, following the evolutionary history of phototrophic species. We begin with a molecular inventory of different thylakoid components and then illustrate how these building blocks are integrated to form membrane networks with diverse architectures. We conclude with an outlook on understanding how thylakoids remodel their architecture and molecular organization during dynamic processes such as biogenesis, repair, and environmental adaptation.

Почвенные водоросли и цианопрокариоты степных сообществ Байкальской котловины

The article presents the results of studies of herbaceous plant communities in the Baikal basin, with the significant participation of the diazotrophic cyanoprokaryota Nostoc commune. The territory of the investigation is located at the foot of the Primorskiy range. There are developed mountain, typical steppe, and meadow communities on chestnut soils. A high content of carbonates was found in the soils, and the pH of the upper horizons varied from slightly acidic to alkaline. The composition of algae and cyanoprokaryota species living in and on soils has been revealed. In total, in steppe and meadow communities we identified 71 species from five divisions: Cyanoprokaryota – 27, Bacillariophyta – 4, Ochrophyta – 3, Chlorophyta – 34, and Charophyta – 3. 58 species have been found in steppe communities, 40 in meadow. A predominance of cyanoprokaryota and green algae was noted. The composition of the studied phototrophic species in steppe communities differed significantly from that of the meadow. In steppe communities Nostoc commune formed macroscopic colonies, and its biomass production was low (about 2 g/m2) comparable to that of a number of Asia arid territories. The N. commune biomass formation was higher on the mountain slope and at its foot, where higher density of soil composition, lower field humidity, as well as an increased content of calcium, magnesium, and sodium was found in soils. The N. commune biomass was reduced in the site at a distance from the mountain slope where the content of the above elements was lower. The regular sampling of macrocolonies had a negative impact on their renewal.

Effects of graphene oxide on the diatom Nitzschia palea are associated with carbon cycling disturbance

Graphene based nanomaterials (GBMs) have been drawing the attention of the scientific communities these past years. As their market is increasing every year, their potential environmental and health risk are to be assessed. As microbial communities represent the basis of every ecosystem, it is essential to evaluate the risks of GBMs on these communities. The effects of GBMs on bacteria has been widely studied, while the effects on phototrophic species are less represented. In this study, the diatom Nitzschia palea was exposed to graphene oxide (GO) and reduced graphene oxide (rGO), at 0.1, 1 and 10 mg L−1. rGO had no effect on the diatom while GO induced an increase in growth, indicating the importance of the oxidation rate in the observed effect. Further results showed that shading effect of GO was countered by increased chlorophyll contents and by the accumulation of GO into the biofilm. This “sticking” mechanism increased the proximity between the biofilm and the GO, which might favour interactions between GO and the biofilm. These interactions led to the increase of defects and the reduction of GO. In addition, increased heterotrophic activity was suggested. To our knowledge, no diatom before Nitzschia palea has been shown to enhance its growth in presence of a GBM, but also capable to modify it. These results demonstrate the potential of GBMs, and in particular those with higher oxidation rates, to disrupt the contribution of the diatom Nitzschia palea to carbon cycling, which could have broader consequences at ecosystem scale.

A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer.

During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.

Single Phototrophic Bacterium-Mediated Iron Cycling in Aquatic Environments

Redox cycling of iron plays a pivotal role in both nutrient acquisition by living organisms and the geochemical cycling of elements in aquatic environments. In nature, iron cycling is mediated by microbial Fe(II)-oxidizers and Fe(III)-reducers or through the interplay of biotic and abiotic iron transformation processes. Here, we unveil a specific iron cycling process driven by one single phototrophic species, Rhodobacter ferrooxidans SW2. It exhibits the capability to reduce Fe(III) during bacterial cultivation. A c -type cytochrome is identified with Fe(III)-reducing activity, implying the linkage of Fe(III) reduction with the electron transport system. R. ferrooxidans SW2 can mediate iron redox transformation, depending on the availability of light and/or organic substrates. Iron cycling driven by anoxygenic photoferrotrophs is proposed to exist worldwide in modern and ancient environments. Our work not only enriches the theoretical basis of iron cycling in nature but also implies multiple roles of anoxygenic photoferrotrophs in iron transformation processes.

Protists in hypoxic waters of Jinhae Bay and Masan Bay, Korea, based on metabarcoding analyses: emphasizing surviving dinoflagellates

Hypoxia can indeed impact the survival of protists, which play a crucial role in marine ecosystems. To better understand the protistan community structure and species that can thrive in hypoxic waters, we collected samples from both the surface and bottom waters during the hypoxic period in Jinhae and Masan Bays and the non-hypoxic period in Jinhae Bay. Subsequently, we utilized metabarcoding techniques to identify the protistan species. During hypoxia, with dissolved oxygen concentrations of 0.8 mg L<sup>-1</sup> in Jinhae Bay and 1.8 mg L<sup>-1</sup> in Masan Bay within the bottom waters, the phylum Dinoflagellata exhibited the highest amplicon sequence variants richness among the identified protist phyla. Following the Dinoflagellata, Ochrophyta and Ciliophora also displayed notable presence. In hypoxic waters of Jinhae and Masan Bays, we identified a total of 36 dinoflagellate species that exhibited various trophic modes. These included one autotrophic species, 14 mixotrophic species, 9 phototrophic species with undetermined trophic modes (either autotrophic or mixotrophic), 2 kleptoplastidic species, and 10 heterotrophic species. Furthermore, the hypoxic bottom water exhibited a greater number of heterotrophic dinoflagellate species compared to the non-hypoxic surface water within the same water column or the non-hypoxic bottom water. Therefore, feeding by mixotrophic and heterotrophic dinoflagellates may be partially responsible for their dominance in terms of the number of species surviving in hypoxic waters. This study not only introduces the initial documentation of 26 dinoflagellate species surviving in hypoxic conditions but also establishes a foundation for a more comprehensive understanding of the ecophysiology of dinoflagellates in hypoxic marine environments.

Effects of elevated temperature and copper exposure on the physiological state of the coral Galaxea fascicularis

The co-occurrence of elevated seawater temperature and local stressors (heavy metal contamination) affects the ecophysiology of phototrophic species, and represents a risk to the environmental quality of coral reefs. Therefore, we investigated the effects of both Cu alone and Cu in combination with elevated temperature (ET) on the physiology of the coral Galaxea fascicularis, and measured the parameters related to the photo-physiology and oxidative state. G.fascicularis is one of the dominant coral species in the South China Sea which exhibits strong adaptability to environmental stress. We exposed the common coral species G.fascicularis to a series of environmentally relevant concentrations of Cu at 29 °C (normal temperature, NT) and 32 °C (elevated temperature, ET) for 96 h. Single polyps were used in the experiments, which reduced individual variability when compared to the coral colonies. The results suggested that: i) Cu or ET had significant negative effects on the actual operating ability of photosystem Ⅱ (PSII), but not on the maximal chlorophyll fluorescence in darkness (Fv/Fm). ii) Symbiodiniaceae density was significantly reduced by high Cu concentrations, for Cu-NT and Cu-ET, a high concentration of Cu (40 μg/L) significantly impacted Symbiodiniaceae density, causing a 75.4% and 81.0% decrease, respectively. iii) the content of malondialdehyde (MDA) in coral tissues increased significantly under Cu-ET. iv) a certain range of copper concentration (25–30 μg/L) increased the pigment content of the Symbiodiniacea. Our results indicated that the combined stressors of Cu and ET made the coral tissue sloughed, caused the coral tissue damaged by lipid oxidation, reduced the photosynthetic capacity of the Symbiodiniacea, and led to the excretion of Symbiodiniacea.

Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

BackgroundMarine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations.ResultsThe most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes.8L85edCQnxTD9xJZeGdCikVideo ConclusionsOur results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.

Phototrophic Colonization in Dolomitic Limestone: Comparison between Single vs Artificial Multispecies

Phototrophic organisms, such as microalgae and cyanobacteria, are known to be major contributors to stone decay. The purpose of this study was to assess the dolomitic limestone colonization by phototrophic organisms, using single vs artificial multispecies, under laboratory conditions. To achieve this aim, dolomitic limestone blocks were inoculated with single phototrophic species previously collected from the Old Cathedral of Coimbra, for a period of three months. In parallel, limestone blocks were also inoculated with a mixture of the same isolated single species, in order to compare the colonization capacities of both conditions. Results were evaluated based on visual inspection, surface covered area, colorimetric and SEM analyses. Results showed that the phototrophic organisms were able to colonize the dolomitic limestone blocks in both conditions (single vs artificial multispecies), but biofilm development was more enhanced when single species, rather than multispecies, were used. The obtained results also allowed to observe the capacity for endolithic colonization and the formation of small cavities by some species.

Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities

Phototrophic biofilms, also known as periphyton, are microbial freshwater communities that drive crucial ecological processes in streams and lakes. Gaining a deep mechanistic understanding of the biological processes occurring in natural periphyton remains challenging due to the high complexity and variability of such communities. To address this challenge, we rationally developed a workflow to construct a synthetic community by co-culturing 26 phototrophic species (i.e., diatoms, green algae, and cyanobacteria) that were inoculated in a successional sequence to create a periphytic biofilm on glass slides. We show that this community is diverse, stable, and highly reproducible in terms of microbial composition, function, and 3D spatial structure of the biofilm. We also demonstrate the ability to monitor microbial dynamics at the single species level during periphyton development and how their abundances are impacted by stressors such as increased temperature and a herbicide, singly and in combination. Overall, such a synthetic periphyton, grown under controlled conditions, can be used as a model system for theory testing through targeted manipulation.

Biocrust diazotrophs and bacteria rather than fungi are sensitive to chronic low N deposition.

Anthropogenic long-term nitrogen (N) deposition may dramatically impact biocrusts due to the overarching N limitation of soil biota in deserts. Even low levels of N may reach a critical loading threshold altering biocrust constituents and function. To identify the impact of chronic and continuous low levels of N deposition on biocrusts, we created a realistic gradient mirroring anthropogenic N addition rate (2:1 NH4 + : NO3 - rates: 0.3, 0.5, 1.0, 1.5, 3g N m-2 yr-1 ) and measured the response of bacteria and fungi within cyanobacterial-dominated biocrusts over 8 years in a temperate desert, the Gurbantunggut Desert, China. We found that once N deposition reached 1.5g N m-2 yr-1 biocrust bacterial communities, including diazotrophs, were altered while no such tipping point existed for fungi. Above the threshold, bacterial richness was enhanced, the relative abundance of Chloroflexi, FBP and Gemmatimonadetes was elevated, and diazotrophs shifted from being dominated by Nostocaceae and Scytonemataceae (Cyanobacteria) to free-living Bradyrhizobiaceae (Alphaproteobacteria). Alternatively, the relative recovery of a few fungal species within the Lecanorales, Pleosporales and Verrucariales became either enriched or diminished due to N deposition. The chronic addition of N resulted in a dense and interconnected bacterial co-occurrence network that accentuated a functional shift from networks dominated by phototrophic species within the Nostocaceae, Xenococcaceae, Phormidiaceae and Scytonemataceae (Cyanobacteria) to ammonia-oxidizing species within the Nitrosomonadaceae (Betaproteobacteria) and nitrifying bacteria [i.e. Nitrospiraceae (Nitrospirae)]. Based on structural equation models, the effects of N additions on biocrust constituents were imposed through indirect effects on pH, soil electrical conductivity and ammonium concentrations. In summary, biocrust constituents are generally insensitive to chronic low levels of N depositions until rates reach above 1.5g N m-2 yr-1 with diazotrophs being the most sensitive biocrust constituents followed by bacteria and finally fungi. Ultimately once the threshold is reached N deposition favours biocrust constituents utilizing inorganic N and other C sources over relying on phototrophic and/or N-fixing cyanobacteria for C and N.

Individual and combined effects of diuron and light reduction on marine microalgae

Coastal ecosystems such as those in the Great Barrier Reef (GBR) lagoon, are exposed to stressors in flood plumes including low light (caused by increased turbidity) and agricultural pesticides. Photosystem II (PSII)-inhibiting herbicides are the most frequently detected pesticides in the GBR lagoon, but it is not clear how their toxicity to phototrophic species depends on light availability. This study investigated the individual and combined effects of PSII-inhibiting herbicide, diuron, and reduced light intensity (as a proxy for increased turbidity) on the marine diatom, Phaeodactylum tricornutum. Effective quantum yield (EQY) and cell density were measured to calculate responses relative to the controls over 72-h, in tests with varying stressor intensities. Individually, diuron concentrations (0.1–3 μg l−1) were not high enough to significantly reduce growth (cell density), but led to decreased EQY; while, low light generally led to increased EQY, but only reduced growth at the lowest tested light intensity (5 μmol photons m−2 s−1) after 48-hours. P. tricornutum was less affected by diuron when combined with low light scenarios, with increased EQY (up to 163% of the controls) that was likely due to increased electron transport per photon, despite lesser available photons at this low light intensity. In contrast, growth was completely inhibited relative to the controls when algae were simultaneously exposed to the highest stressor levels (3 μg l−1 diuron and 5 μmol photons m−2 s−1). This study highlights the importance of measuring more than one biological response variable to capture the combined effects of multiple stressors. Management of water quality stressors should consider combined impacts rather than just the impacts of individual stressors alone. Reducing suspended sediment and diuron concentrations in marine waters can decrease harmful effects and bring synergistic benefits to water quality.

Remarkably coherent population structure for a dominant Antarctic Chlorobium species

BackgroundIn Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function.ResultsA single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml−1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts.ConclusionThe factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.FJebgLEuwcBu4fPtsFrHHTVideo abstract

Redesigning the photosynthetic light reactions to enhance photosynthesis - the PhotoRedesign consortium.

In this Perspective article, we describe the visions of the PhotoRedesign consortium funded by the European Research Council of how to enhance photosynthesis. The light reactions of photosynthesis in individual phototrophic species use only a fraction of the solar spectrum, and high light intensities can impair and even damage the process. In consequence, expanding the solar spectrum and enhancing the overall energy capacity of the process, while developing resilience to stresses imposed by high light intensities, could have a strong positive impact on food and energy production. So far, the complexity of the photosynthetic machinery has largely prevented improvements by conventional approaches. Therefore, there is an urgent need to develop concepts to redesign the light-harvesting and photochemical capacity of photosynthesis, as well as to establish new model systems and toolkits for the next generation of photosynthesis researchers. The overall objective of PhotoRedesign is to reconfigure the photosynthetic light reactions so they can harvest and safely convert energy from an expanded solar spectrum. To this end, a variety of synthetic biology approaches, including de novo design, will combine the attributes of photosystems from different photoautotrophic model organisms, namely the purple bacterium Rhodobacter sphaeroides, the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana. In parallel, adaptive laboratory evolution will be applied to improve the capacity of reimagined organisms to cope with enhanced input of solar energy, particularly in high and fluctuating light.

Effect of zero-valent iron and granular activated carbon on nutrient removal and community assembly of photogranules treating low-strength wastewater

Traditional wastewater treatment processes with high energy consumption and greenhouse gas emissions are not suitable for rural areas with low sewage strength and wide distribution. In this study, a microalgae-bacteria synergistic photogranules system was developed under the impetus of green chemical additives to address these challenges. The results showed that zero-valent iron (ZVI) or granular activated carbon (GAC) addition made successful photogranulation treating low-strength wastewater with excellent settleability and stability performance (settling velocity: 14–22 m h−1; integrity coefficient: 0.81–6.62%), while systems without light or additives failed due to the bio-granules disintegration caused by the overgrowth of predators or phototrophic species. A better nutrient removal performance (TN < 15 mg L−1, TP < 0.4 mg L−1) was observed in photogranules systems, and stoichiometric and biological analysis found that the divisions of nitrogen removal by microalgae and bacteria were different for photogranules between GAC and ZVI additions. As a physical enhancer, GAC can be used as the nucleus of photogranules regenerating after granules disintegration rather than affecting the community succession process. However, ZVI addition strengthened the sedimentation ability and stability of photogranules through chemical and biological effects, focusing on enhancing bacterial community diversity, enriching biofilm formation bacteria and inhibiting the overgrowth of filamentous cyanobacteria. Notably, the photogranules process with ZVI addition could be operated under non-aeration conditions without compromising removal efficiency. There existed an ideal distribution of microalgae and bacterial functional species in the photogranules, which seemed to be essential for its self-sustained synergistic symbiosis and stability. Consequently, this work might provide engineering alternatives for realizing carbon neutrality and environmental sustainability of the decentralized wastewater treatment process for low-strength wastewater in rural areas.

Selecting phototrophic species of native biocrusts in arid and semi-arid regions

Background: Biological soil crusts (BSCs) that are able to produce sticky extracellular polymeric substances (EPS) play an important role in the formation of soil aggregates, thereby, reducing soil erosion. In this study, experiments were undertaken to identify biocrust species that produce EPS, in order to combat desertification in the Sejzi desert of Iran. Methods: A biocrust distribution map of Sejzi plain was prepared using Landsat 8 OLI images, then, various sampling points were selected. Some physicochemical parameters of samples from lichen-dominated and non-biocrusted areas were measured. The relationship between soil parameters and biocrusts presence was confirmed based on the Pearson’s correlation coefficient and principal component analysis (PCA) method. The type of chemical compounds in the soil content were determined via Fourier transform infrared spectroscopy (FTIR), including polysaccharides. To estimate the degradability of polysaccharides, each soil sample was placed under defined UV-B radiation for 24, 48, and 72 hours at three replications. Results: There was no significant correlation between moss and lichen species with the amount of EPS (%) values and various occurring cyanolichen species in three biocrusted soil samples, which included Collema coccophorum, Collema tenax, Peccania terricola, and Placidium squamulosum. It was speculated that these polysaccharides were produced by the photobiotic partners (microalgae or cyanobacteria) and secreted to the soil. Conclusion: According to the results, the cyanobacteria species of biocrusted samples might have high potential to combat desertification and soil stabilization in Sejzi desert.

Contribution of biological soil crusts to soil organic matter composition and stability in temperate forests

Biological soil crusts (biocrusts) play an important role in the biogeochemical C-, N- and P-cycles but there is limited knowledge about their effect on the composition and stability of organic matter (OM) in soil. In pine and beech dominated temperate forests, the different compartments of biocrust, crust-adhering soil and crust-free soil were analysed by pyrolysis field ionization mass spectrometry (Py-FIMS) and C K-edge X-ray absorption near edge structure (XANES) spectroscopy. Phototrophic biocrust communities had been determined morphologically. Predominant tree species affected OM composition and stability but an overriding effect of biocrust organisms was observed. In biocrusts, the OM mineralization potential was high due to a high carbohydrate/ketone ratio and a high proportion of the fatty acid C22:0. A high proportion of free fatty acids in combination with a high carbohydrate proportion was identified as a relative marker for biocrusts and additional high proportions of lignin dimers were specific for samples under pine. In biocrust under pine, OM in soil compartments was characterized by large proportions of long-chain aliphatics from plant cuticular material. In A-horizon substrate under beech, OM compound classes were not affected by phototrophic species richness, suggesting functional redundancy of these biocrust organisms with regard to OM composition. In contrast to A-horizon substrate, OM in C-horizon substrate was characterized by a higher proportion of easily decomposable material. Under pine, forest management intensity (SMI) affected OM by stand age and density due to effects on phototrophic biocrust species. We conclude that compartment, vegetation, horizon substrate and SMI affected OM composition and stability, and biocrusts hence contributed to soil OM diversity in forest ecosystems.

Temporal and spatial variability of phytoplankton and mixotrophs in a temperate estuary

A significant proportion of phototrophic species are known to be mixotrophs: cells that obtain nutrients through a combination of photosynthesis and prey ingestion. Current methods to estimate mixotroph abundance in situ are known to be limited in their ability to help identify conditions that favor mixotrophs over strict autotrophs. For the first time, we combine microscopic analysis of phototrophic taxa with immunoprecipitated bromodeoxyuridine (BrdU)-labeled DNA amplicon sequencing to identify and quantify active and putative mixotrophs at 2 locations in a microtidal temperate estuary. We analyze these data to examine spatial and temporal variability of phytoplankton and mixotrophs. Microscopy-based phototrophic diversity and abundances reveal expected seasonal patterns for our 2 stations, with the start of growth in winter and highest abundances in summer. Diatoms tend to dominate at the site with less stratification, while dinoflagellates and euglenids are usually more prominent at the stratified station. The BrdU-based mixotroph identifications are translated to the microscopy identification and abundances to estimate the proportion of mixotrophs (cells &gt;10 µm in size) at both sites. The average proportion of potential mixotrophs is higher at the station with higher stratification (51%) compared to the station with lower stratification (30%), and potential mixotrophs tend to be higher in summer, although we did not conduct BrdU experiments in any of the other seasons. Combining the identification of active mixotrophs through the uptake of BrdU-labeled bacteria with robust abundance measurements can expand our understanding of mixotrophs across systems.

Utilization of light energy in phototrophic Gemmatimonadetes

Gemmatimonas phototrophica is, so far, the only described phototrophic species of the bacterial phylum Gemmatimonadetes. Its cells contain a unique type of photosynthetic complex with the reaction center surrounded by a double ring antenna, however they can also grow in the dark using organic carbon substrates. Its photosynthesis genes were received via horizontal gene transfer from Proteobacteria. This raises two questions; how the horizontally transferred photosynthesis apparatus has integrated into the cellular machinery, and how much light-derived energy actually contributes to the cellular metabolism? To address these points, the photosynthetic reactions were studied on several levels, from photophysics of the reaction center to cellular growth. Flash photolysis measurements and bacteriochlorophyll fluorescence kinetic measurements documented the presence of fully functional type-2 reaction centers with a large light harvesting antenna. When illuminated, the bacterial cells reduced their respiration rate by 58 ± 5%, revealing that oxidative phosphorylation was replaced by photophosphorylation. Moreover, illumination also more than doubled the assimilation rates of glucose, a sugar that is mostly used for respiration. Finally, light increased the growth rates of Gemmatimonas phototrophica colonies on agar plates. All the presented data provide evidence that photosynthetic complexes are fully integrated into cellular metabolism of Gemmatimonas phototrophica, and are able to provide a substantial amount of energy for its metabolism and growth.

Interocean patterns in shallow water sponge assemblage structure and function.

Sponges are a major component of benthic ecosystems across the world and fulfil a number of important functional roles. However, despite their importance, there have been few attempts to compare sponge assemblage structure and ecological functions across large spatial scales. In this review, we examine commonalities and differences between shallow water (<100 m) sponges at bioregional (15 bioregions) and macroregional (tropical, Mediterranean, temperate, and polar) scales, to provide a more comprehensive understanding of sponge ecology. Patterns of sponge abundance (based on density and area occupied) were highly variable, with an average benthic cover between ~1 and 30%. Sponges were generally found to occupy more space (percentage cover) in the Mediterranean and polar macroregions, compared to temperate and tropical macroregions, although sponge densities (sponges m-2 ) were highest in temperate bioregions. Mean species richness standardised by sampling area was similar across all bioregions, except for a few locations that supported very high small-scale biodiversity concentrations. Encrusting growth forms were generally the dominant sponge morphology, with the exception of the Tropical West Atlantic, where upright forms dominated. Annelids and Arthropods were the most commonly reported macrofauna associated with sponges across bioregions. With respect to reproduction, there were no patterns in gametic development (hermaphroditism versus gonochorism), although temperate, tropical, and polar macroregions had an increasingly higher percentage of viviparous species, respectively, with viviparity being the sole gamete development mechanism reported for polar sponges to date. Seasonal reproductive timing was the most common in all bioregions, but continuous timing was more common in the Mediterranean and tropical bioregions compared to polar and temperate bioregions. We found little variation across bioregions in larval size, and the dominant larval type across the globe was parenchymella. No pattens among bioregions were found in the limited information available for standardised respiration and pumping rates. Many organisms were found to predate sponges, with the abundance of sponge predators being higher in tropical systems. While there is some evidence to support a higher overall proportion of phototrophic species in the Tropical Austalian bioregion compared to the Western Atlantic, both also have large numbers of heterotrophic species. Sponges are important spatial competitors across all bioregions, most commonly being reported to interact with anthozoans and algae. Even though the available information was limited for many bioregions, our analyses demonstrate some differences in sponge traits and functions among bioregions, and among macroregions. However, we also identified similarities in sponge assemblage structure and function at global scales, likely reflecting a combination of regional- and local-scale biological and physical processes affecting sponge assemblages, along with common ancestry. Finally, we used our analyses to highlight geographic bias in past sponge research, and identify gaps in our understanding of sponge ecology globally. By so doing, we identified key areas for future research on sponge ecology. We hope that our study will help sponge researchers to consider bioregion-specific features of sponge assemblages and key sponge-mediated ecological processes from a global perspective.