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Heterotrophic CO2 fixation is a significant yet underappreciated CO2 flux in environmental carbon cycling. In contrast to photosynthesis and chemolithoautotrophy – the main recognized autotrophic CO2 fixation pathways – the importance of heterotrophic CO2 fixation remains enigmatic. All heterotrophs – from microorganisms to humans – take up CO2 and incorporate it into their biomass. Depending on the availability and quality of growth substrates, and drivers such as the CO2 partial pressure, heterotrophic CO2 fixation contributes at least 1 %–5 % and in the case of methanotrophs up to 50 % of the carbon biomass. Assuming a standing stock of global heterotrophic biomass of 47–85 Pg C, we roughly estimate that up to 5 Pg C might be derived from heterotrophic CO2 fixation, and up to 12 Pg C yr−1 originating from heterotrophic CO2 fixation is funneled into the global annual heterotrophic production of 34–245 Pg C yr−1. These first estimates on the importance of heterotrophic fixation of inorganic carbon indicate that this pathway should be incorporated in present and future carbon cycling budgets.

Cyanobacteria, which use solar energy to convert carbon dioxide into biomass, are potential solar biorefineries for the sustainable production of chemicals and biofuels. However, yields obtained with current strains are still uncompetitive compared to existing heterotrophic production systems. Here we report the discovery and characterization of a new cyanobacterial strain, Synechococcus sp. PCC 11901, with promising features for green biotechnology. It is naturally transformable, has a short doubling time of ≈2 hours, grows at high light intensities and in a wide range of salinities and accumulates up to ≈33 g dry cell weight per litre when cultured in a shake-flask system using a modified growth medium − 1.7 to 3 times more than other strains tested under similar conditions. As a proof of principle, PCC 11901 engineered to produce free fatty acids yielded over 6 mM (1.5 g L −1 ), an amount comparable to that achieved by similarly engineered heterotrophic organisms. Włodarczyk et al. discover that cyanobacterium Synechococcus sp . PCC 11901 accumulates three times more biomass than other cyanobacterial strains in the same conditions. An engineered version of this strain also produces as much free fatty acid as other commonly used heterotrophic microorganisms, suggesting its utility for the sustainable production of carbon-based molecules.

Microorganisms that transform and oxidize organic material (that is, heterotrophs) play a fundamental role in the geochemical cycling of key elements in the ocean. Through their growth and activity, heterotrophic microorganisms degrade much of the organic matter produced by phytoplankton in the surface ocean, leading to the regeneration and redistribution of nutrients and carbon back into the water column. However, most organic matter is physically too large to be taken up directly by heterotrophic microorganisms. Consequently, many heterotrophs secrete exoenzymes that break down large molecules outside the cell into smaller substrates that can then be directly taken up by the cell. The complex nature of the biochemical systems that microorganisms use to secrete these enzymes suggests that they were unlikely to have been present in the earliest heterotrophs. In a pre-exoenzyme ocean, heterotrophic microorganisms would only be able to access a small fraction of organic matter such that most dead phytoplankton biomass would have passed directly through the water column and settled onto the seafloor. Here we synthesize existing geobiological evidence to examine the fate of organic matter in the absence of exoenzymes in early oceans. We propose that on an Earth before exoenzymes, organic matter preservation, metal availability and phosphorus recycling would have operated differently than they do on the contemporary Earth.Exoenzymes produced by heterotrophic microorganisms early in Earth history helped unlock previously unavailable organic matter and transformed ocean geochemistry.

Biofilms were cultivated for a 68-day period under different hydrodynamic conditions, and the effect of hydrodynamics on the succession of autotrophic and heterotrophic organisms of biofilms was investigated. Five obvious stages were observed during biofilm formation. At Stage I, the attachment of algae was delayed, especially under turbulent conditions. After Stage II, algal density and heterotrophic biomass of biofilms increased, which were obvious under turbulent flow. Therefore, the algal density and heterotrophic biomass of biofilms were largest under turbulent condition, followed by laminar condition, and then transitional condition. Diatoms were dominant in all flumes and were most abundant under turbulent conditions. The proportion of cyanobacteria was highest under laminar conditions. The ratio of aerobic to anaerobic bacteria decreased and their co-existence could facilitate the nitrification and denitrification in the biofilm. The ratio of monounsaturated fatty acids to saturated fatty acids was highest under turbulent conditions on the 15th day. While the ratio was highest under laminar condition on the 48th day, the high ratio indicates the high ability of biofilm to obtain nutrients, which affect the growth of algae. The regulation of hydrodynamics is a useful technology which can affect the growth of the microorganisms of biofilm, and further improve water quality.

Phototrophic biofilms are complex conglomerations of light-driven microorganisms as autotrophs with heterotrophs embedded in a mucilaginous matrix comprising EPS (extracellular polymeric substances), attached to a solid surface. EPS provide structural and functional integrity and is essential for the physico-chemical and biological properties of the biofilms. These biofilms thrive in simple to extreme environments and comprise cyanobacteria, diatoms, microalgae, fungi, bacteria and protozoa. Formation of flocs/biofilms is an essential facet of bioremediation and wastewater treatment. Biofilm formation is a scourge in medical sciences, but in agriculture, they can be potent candidates for integrated nutrient and disease management or soil structure improvement, as they aid in better and effective colonization in soil and around roots, enabling a network from soil to the plant. The process of biofilm formation is intriguing and presents a challenge for understanding the signals and metabolites involved and the orchestration of multiple biochemical pathways. Metagenomic analysis of biofilms has unveiled complex genomic data and molecular diversity among culturable and non-culturable microbial communities dwelling in such biofilms; however, information on phototrophic biofilms is scanty. Particle-tracking techniques have shown the significance of water channels in mediating water flow, nutrient cycling and exchange of metabolites within the biofilm community. Proteomic analyses and their bioinformatic delineation have illustrated that in these biofilms, the phototrophic partner is involved in intercellular signaling, aggregation, carbohydrate and amino acid metabolism. The present review focuses on phototrophic biofilm formation, their diversity, applications and ecological roles with special emphasis on agriculture and allied sectors.

A pilot scale biological nutrient removal (BNR) process, batch experiments and modeling exercises were employed to investigate the removal and biotransformation of trimethoprim (TMP) in a BNR activated sludge process. The concentrations of the active microbial groups – ammonia oxidizing bacteria (AOB), ordinary heterotrophic organisms (OHOs) and polyphosphate accumulating organisms (PAOs) – in the BNR bioreactor were quantified through modeling of the pilot bioreactor. The overall TMP removal efficiency for the pilot BNR process was 64 ± 14% while the TMP biotransformation efficiencies in the anaerobic, anoxic and aerobic zones were 22 ± 20%, 27 ± 8% and 36 ± 5% respectively. Batch tests with and without nitrification inhibition showed that AOB played a role in the biotransformation of TMP in BNR activated sludge. A pseudo first order model which incorporated the contributions of PAOs, OHOs and AOB to the overall biodegradation of TMP was found to describe the biodegradation of TMP in batch tests with and without nitrification inhibition. This model showed that PAOs, OHOs and AOB contributed towards the biotransformation of TMP in aerobic BNR activated sludge with the biotransformation rate constants following the trend of kAOB > kOHOs > kPAOs.

Schembri, S. and Zammit, G., 2022. The biodiversity of epilithic microalgal communities colonising a central Mediterranean coastline. Journal of Coastal Research, 38(2), 249–260. Coconut Creek (Florida), ISSN 0749-0208. Microbial communities colonise the coastal ecosystem around the Maltese islands. However, such communities are understudied, both in Malta and in the central Mediterranean. This research aims to increase current knowledge about the biodiversity of phototrophic communities growing along a central Mediterranean rocky shoreline and is the first such study to be performed on microorganisms growing in epilithic biofilms and microbial mats along the coastline in the Maltese islands. Samples were obtained using techniques that were noninvasive to the underlying substratum. These were studied by direct observation using light and electron microscopy, by culturing in vitro, by molecular analysis via sequencing of the small subunit ribosomal ribonucleic acid genes and phylogenetic analyses. Microscopic analyses revealed highly diverse communities made of both photosynthetic and heterotrophic organisms. The predominant microorganisms were simple filamentous cyanobacteria including species of Leptolyngbya, Phormidesmis, Nodosilinea, Toxifilum, Phormidium, and Lyngbya, as well as heterocytous Calothrix and Nunduva spp. The coccal cyanobacteria included species of Aphanocapsa and Chroococcus, whereas coccal microalgae belonged to Chlorella, Chlamydomonas, and Coelastrella spp., accompanied by diatoms of Navicula sp. These results include first records of cyanobacterial and microalgal barcodes that were genetically sequenced from a coastline in the central Mediterranean. Germlings of the filamentous macroalga Cladophora were embedded in the rocky substrate that was preconditioned by biofilm growth and ciliated protozoans, micronematodes, and microcrustaceans interacted with the microbial communities. The isolation of new cyanobacterial and microalgal strains from these phototrophic communities highlights the importance of employing a combined multiphasic approach to supplement current knowledge about the biodiversity of microbial communities colonising rocky shores.

Photosynthetic microorganisms are important components of most ecosystems and have important roles regarding biogeochemical cycles and the basis of the trophic chain. However, they sometimes are present in low abundance compared to other heterotrophic organisms. The Chapada das Mesas National Park (PNCM) is a Conservation Unit in Brazilian Cerrado biome, which is considered a hotspot for biodiversity conservation and possesses important rivers, waterfalls, and springs with economical and touristic importance. The aim of this study was to perform a comparative analysis of enriched and total microbiome of sediments to understand the impact of pre-cultivation in discovery of underrepresented groups like photosynthesizers. All sediment samples were cultivated in BG-11 medium under illumination to enrich for photosynthetic microorganisms and both the raw samples and the enriched ones were submitted to DNA extraction and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene on the Ion Torrent platform. The reads were analyzed using QIIME2 software and the Phyloseq package. The enrichment allowed detection and identification of many genera of cyanobacteria in the Chapada das Mesas National Park (PNCM), which would probably not be possible without the combination of approaches. A total of 58 groups of photosynthetic microorganisms were classified in the samples from the enrichments and their relative abundance based on amplified 16S rRNA sequences were estimated, highlighting the genus Synechocystis which represented 10.10% of the abundance of the phylum Cyanobacteria and the genus Dunaliella , which represented 45.66% of the abundance of algae as the most abundant groups at the PNCM. In the enrichments, microorganisms from the phyla Proteobacteria (45.2%), Bacteroidetes (18%), and Planctomycetes (3.3%) were also identified, since there are ecological associations between the photosynthetic community and other groups of heterotrophic microorganisms. As for the functional analysis, metabolic functions associated with methanotrophy and methylotrophy, hydrocarbon degradation, phototrophy, and nitrogen fixation were predicted. The results highlight a great diversity of photosynthetic microorganisms in Cerrado and the importance of using a combination of approaches when analyzing target groups which are usually underrepresented such as cyanobacteria and microalgae.

Iron (Fe) is a paradox in the modern ocean—it is central to many life-critical enzymes but is scarce across most surface waters. The high cellular demand and low bioavailability of Fe likely puts selective pressure on marine microorganisms. Previous observations suggest that heterotrophic bacteria are outcompeted by small diatoms for Fe supply in the SubAntarctic Zone of Southern Ocean, thereby challenging the idea of heterotrophic bacteria being more competitive than phytoplankton in the access to this trace metal. To test this hypothesis, incubation experiments were carried out at the Southern Ocean Time Series site (Mar.–Apr. 2016). We investigated (a) whether dissolved organic carbon (DOC), dissolved Fe, or both limit the growth of heterotrophic bacteria and, (b) if the presence of potential competitors has consequences on the bacterial Fe acquisition. We observed a pronounced increase in both bulk and cell-specific bacterial production in response to single (+C) and combined (+Fe+C) additions, but no changes in these rates when only Fe was added (+Fe). Moreover, we found that +Fe+C additions promoted increases in cell-specific bacterial Fe uptake rates, and these increases were particularly pronounced (by 13-fold) when phytoplankton were excluded from the incubations. These results suggest that auto- and heterotrophs could compete for Fe when DOC limitation of bacterial growth is alleviated. These interactions between primary producers and nutrient-recyclers are unexpected drivers for the duration and magnitude of phytoplankton blooms in the Southern Ocean.

As the ecologically important recipient channels for riverine ecosystems, tributaries provide unique microhabitats for microorganisms, among which zooplankton constitutes the most important heterotrophic organisms. In particular, the reduced water velocity caused by dams is more favorable for zooplankton development; therefore, dammed rivers are expected to support extremely diverse and abundant zooplankton communities and notably different spatiotemporal distribution patterns. So far, however, only very few molecular studies support these assumptions. Using high-throughput sequencing, a high number of 350 operational taxonomic units (OTUs; 97% cutoff) were retrieved from 30 samples collected in the Xiangxi River, the nearest large tributary upstream of the Three Gorges Dam. Zooplankton did not show significant spatial distribution in the channel. Instead, the community structures varied significantly over sampling dates, corroborating the seasonal patterns found in lakes and ponds in the subtropical zone. As expected, the community compositions were deterministically governed by environmental filtering processes (phylogenetic clustering), in which water velocity appeared to be much less important than other investigated environmental factors. Moreover, most of the detected phylotypes (OTUs) had a relatively high (>90%) sequence similarity to previously deposited sequences, suggesting a mediocre degree of genetic novelty within the zooplankton communities in the Xiangxi River.