Composition of microorganisms in carbonated mineral waters of the Mukhen deposit (Khabarovsk territory)

The chemical composition, distribution, structure, number of physiological groups of cultivated bacteria and their biodiversity in the cold carbonic mineral waters of Mukhen and in microbial mats were studied. It is shown that the mineral waters are cold, hydrocarbonate-calcium-magnesium, enriched with iron, manganese, barium. Carbon dioxide predominates in the gaseous composition of waters. Microbiological studies have shown that no sanitary-indicative microflora was found in mineral waters, which indicates the purity of underground waters. Carbonic waters were characterized by a low number of physiological groups of autochthonous bacteria. Among the studied microorganisms, chemolithotrophic thionic bacteria predominated, which indicates the predominance of oxidation processes of reduced sulfur compounds with the participation of bacteria in groundwater. In the microbial mats, various chemolithotrophic and heterotrophic microorganisms were identified, participating in the geochemical cycles of carbon, nitrogen, sulfur, iron, manganese, and silicon. The number of physiological groups of bacteria was higher than in mineral waters, along with this saprophytic bacteria predominated significantly. A sufficiently high rate of protein and cellulose decomposition by microorganisms of microbial mats was shown. A low diversity of cultured heterotrophic bacteria with the dominance of microorganisms of the genus Bacillus was found in mineral waters and in microbial mats. By using the methods of X-ray phase analysis, the important role of microorganisms of microbial mats in the precipitation of silicate minerals and the formation of calcium carbonates was shown.

Biofloc Microbiome With Bioremediation and Health Benefits

The biofloc system has recently attracted great attention as a cost-effective, sustainable, and environmentally friendly technology and expected to contribute toward human food security (Zero Hunger SDG 2). It is also expected that this endeavor can be adopted widely because of its characteristics of zero water exchange and reduced artificial feeding features. In the biofloc system, the flocs which are generally formed by aggregation of heterotrophic microorganisms, serve as natural bioremediation candidates. These microbes effectively maintain water quality by utilizing the nutrient wastes, mostly originated from digested, unconsumed, and metabolic processes of feed. Additionally, the flocs are important sources of nutrients, mainly a protein source, and when these are consumed by aquaculture animals they improve the growth performance, immunity, and disease tolerance of host against pathogenic microbial infection. Here in this review, we focus on recent advances that could provide a mechanistic insight on how the microbial community developed in the biofloc system helps in the bioremediation process and enhances the overall health of the host. We have also tried to address the possible role of these microbial communities against growth and virulence of pathogenic microbes.

Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO2 to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6–23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8–28.4%), pyruvate (9.5%; 4.2–14.8%), and leucine (5.9%; 0.1–11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO2 from respiration unbalanced by net primary production was by 3.69 × 109 g CO2 lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.

Antarctolichenia onofrii gen. nov. sp. nov. from Antarctic Endolithic Communities Untangles the Evolution of Rock-Inhabiting and Lichenized Fungi in Arthoniomycetes

Microbial endolithic communities are the main and most widespread life forms in the coldest and hyper-arid desert of the McMurdo Dry Valleys and other ice-free areas across Victoria Land, Antarctica. There, the lichen-dominated communities are complex and self-supporting assemblages of phototrophic and heterotrophic microorganisms, including bacteria, chlorophytes, and both free-living and lichen-forming fungi living at the edge of their physiological adaptability. In particular, among the free-living fungi, microcolonial, melanized, and anamorphic species are highly recurrent, while a few species were sometimes found to be associated with algae. One of these fungi is of paramount importance for its peculiar traits, i.e., a yeast-like habitus, co-growing with algae and being difficult to propagate in pure culture. In the present study, this taxon is herein described as the new genus Antarctolichenia and its type species is A. onofrii, which represents a transitional group between the free-living and symbiotic lifestyle in Arthoniomycetes. The phylogenetic placement of Antarctolichenia was studied using three rDNA molecular markers and morphological characters were described. In this study, we also reappraise the evolution and the connections linking the lichen-forming and rock-inhabiting lifestyles in the basal lineages of Arthoniomycetes (i.e., Lichenostigmatales) and Dothideomycetes.

Variability of the Sea Surface Microlayer Across a Filament’s Edge and Potential Influences on Gas Exchange

Major uncertainties in air-sea gas flux parameterizations may arise from a yet unpredictable sea surface microlayer (SML). Its influence on gas exchange is twofold as organic matter, in particular surfactants, on one side and organisms enriched in the SML on the other can alter air-sea gas fluxes. However, spatial heterogeneity of the SML and its potential consequences for gas exchange are not well understood. This study examines the SML’s surfactant pool and the dynamics of microbial enrichment across the sharp hydrological front of a newly upwelled filament off Mauritania. The front was marked by a distinct decrease in temperature and salinity compared to the stratified water column outside the filament. Distinct chemical and microbial SML properties were observed and associated with the filament. Overall, organic matter in the SML was significantly higher concentrated inside the filament and in equivalence to the underlying water. Degradation indices derived from total amino acids (TAA) composition indicated production of fresh organic matter inside and increased degradation outside the filament. Moreover, a shift in the microbial community was observed, for instance Synechococcus spp. prevailed outside the filament. Autotrophic and heterotrophic microorganisms preferably colonized the SML outside the filament. Organic matter enrichment in the SML depended largely on the chemical nature of biomolecules. Total organic carbon (TOC), total nitrogen and total combined carbohydrates were only slightly enriched while glucose, TAA and surfactants were considerably enriched in the SML. Surfactant concentration was positively correlated to TAA, in particular to arginine and glutamic acid, indicating that fresh organic matter components enhanced surface activity. Further, TOC and surfactant concentration correlated significantly (r2 = 0.47, p-value < 0.001). The lower limit of this linear correlation hits approximately the lowest TOC concentration expected within the global surface ocean. This suggests that surfactants are primarily derived from autochthonous production and most refractory components are excluded. Using a previously established relationship between surfactants and CO2 gas exchange (Pereira et al., 2018), we estimated that surfactants suppressed gas exchange by 12% inside the filament. This could be of relevance for freshly upwelled filaments, which are often supersaturated in greenhouse gases.

Biohydrometallurgy for Rare Earth Elements Recovery from Industrial Wastes

Biohydrometallurgy recovers metals through microbially mediated processes and has been traditionally applied for the extraction of base metals from low-grade sulfidic ores. New investigations explore its potential for other types of critical resources, such as rare earth elements. In recent times, the interest in rare earth elements (REEs) is growing due to of their applications in novel technologies and green economy. The use of biohydrometallurgy for extracting resources from waste streams is also gaining attention to support innovative mining and promote a circular economy. The increase in wastes containing REEs turns them into a valuable alternative source. Most REE ores and industrial residues do not contain sulfides, and bioleaching processes use autotrophic or heterotrophic microorganisms to generate acids that dissolve the metals. This review gathers information towards the recycling of REE-bearing wastes (fluorescent lamp powder, spent cracking catalysts, e-wastes, etc.) using a more sustainable and environmentally friendly technology that reduces the impact on the environment.

Modeling granule-based completely autotrophic nitrogen removal over the nitrite (CANON) process in an SBR

Based on the simplified activated sludge model No. 1 (ASM1), a 1D biofilm model containing autotrophic microorganisms and heterotrophic microorganisms was developed to describe the microbial population dynamics and reactor dynamics of CANON SBR. After sensitivity analysis and calibration for parameters, the simulation results of NH4+-N concentration and NO2−-N concentration were consistent with the measured results, while the simulated NO3−-N concentration was slightly lower than the measured. The simulation results showed that the soluble microbial products had an extremely low concentration. The aerobic ammonia oxidation bacteria and anaerobic ammonia oxidation bacteria were the dominant microbial populations of the CANON system, while nitrite oxidization bacteria and heterotrophic bacteria were eliminated completely. The optimal ratio of air aeration load to influent NH4+-N load was about 0.18 L air/mgN. The operation condition of the reactor was optimized according to the simulation results, and the total nitrogen removal rate and the total nitrogen removal efficiency increased from 0.312 ± 0.015 to 0.485 ± 0.013 kg N/m3/d and from 71.2 ± 4.3 to 85.7 ± 1.4%, respectively.

Organic Matter in Framboids

Organic matter is intrinsically related to framboids since the sulfide in sedimentary pyrite is almost wholly the result of microbial sulfate reduction by mainly heterotrophic microorganisms. However, framboids do not represent fossil bacteria. The organic matter extracted from framboids tends to take on the form of the pyrite, rather than vice versa. The exact nature of this organic material is unknown. However, it appears that microbial biofilm may be an important contributor. Likewise, the organic residues from some framboids often appear similar to sulfur-rich organic geopolymers such as protokerogen. Most of the organic matter in framboids appears to be syngenetic with the framboids, and some framboids seem to have grown in organic substrates.

Diatom Dominance Enhances Resistance of Phytoplanktonic POM to Mesopelagic Microbial Decomposition

Particulate organic matter (POM) lability is one of the key factors determining the residence time of organic carbon (OC) in the marine system. Phytoplankton community composition can influence the rate at which heterotrophic microorganisms decompose phytoplankton detrital particles and thus, it controls the fraction of OC that reaches the ocean depths, where it can be sequestered for climate-relevant spans of time. Here, we compared the degradation dynamics of POM from phytoplankton assemblages of contrasting diatom dominance in the presence of mesopelagic prokaryotic communities during a 19-day degradation experiment. We found that diatom-derived POM exhibited an exponential decay rate approximately three times lower than that derived from a community dominated by flagellated phytoplankton (mainly coccolithophores and nanoflagellates). Additionally, dissolved organic matter (DOM) released during the degradation of diatom particles accumulated over the experiment, whereas only residual increases in DOM were detected during the degradation of non-diatom materials. These results suggest that diatom-dominance enhances the efficiencies of the biological carbon pump and microbial carbon pump through the relatively reduced labilities of diatom particles and of the dissolved materials that arise from their microbial processing.

Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria

Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day–1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.