Adaptation of Coccomyxa sp. to Extremely Low Light Conditions Causes Deep Chlorophyll and Oxygen Maxima in Acidic Pit Lakes

Aluminum Biorecovery from Wastewaters

Aluminum biorecovery is still at an early stage. However, a significant number of studies showing promising results already exist, although they have revealed problems that need to be solved so aluminum biorecovery can have a wider application and industrial upscaling. In this chapter, we revise the existing knowledge on the biorecovery of aluminum from different sources. We discuss the design, overall performance, advantages, technical problems, limitations, and possible future directions of the different biotechnological methods that have been reported so far. Aluminum biorecovery from different sources has been studied (i.e., solid wastes and primary sources of variable origin, wastewater with low concentrations of dissolved aluminum at pH-neutral or weakly acidic conditions, and acidic mine waters with high concentrations of dissolved aluminum and other metal(loid)s) and has shown that the process efficiency strongly depends on factors such as (1) the physicochemical properties of the source materials, (2) the physiological features of the used (micro)organisms, or (3) the biochemical process used. Bioleaching of aluminum from low-grade bauxite or red mud can much be achieved by a diverse range of organisms (e.g., fungi, bacteria) with different metabolic rates. Biorecovery of aluminum from wastewaters, e.g., domestic wastewater, acidic mine water, has also been accomplished by the use of microalgae, cyanobacteria (for domestic wastewater) or by sulfate-reducing bacteria (acidic mine water). In most of the cases, the drawback of the process is the requirement of controlled conditions which involves a continuous supply of oxygen or maintenance of anoxic conditions which make aluminum biorecovery challenging in terms of process design and economical value. Further studies should focus on studying these processes in comparison or in combination to existing economical processes to assess their feasibility.

Metagenomic insight into the acidophilic functional communities driving elemental geochemical cycles in an acid mine drainage lake

Acidophiles play a key role in the generation, evolution and attenuation of acid mine drainage (AMD), which is characterized by strong acidity (pH<3.5) and high metal concentrations. In this study, the seasonal changes of acidophilic communities and their roles in elemental cycling in an AMD lake (pH∼3.0) in China were analyzed through metagenomics. The results showed eukaryotic algae thrived in the lake, and Coccomyxa was dominant in January (38.1%) and May (33.9%), while Chlorella in July (9.5%). The extensive growth of Chlamydomonas in December (22.7%) resulted in an ultrahigh chlorophyll a concentration (587 μg/L), providing abundant organic carbon for the ecosystem. In addition, the iron-oxidizing and nitrogen-fixing bacterium Ferrovum contributed to carbon fixation. Ammonia oxidation likely occurred in the acidic lake, as was revealed by archaea Ca. Nitrosotalea. To gain a competitive advantage in the nutrient-poor environment, some acidophiles exhibited facultative characteristics, e.g. the most abundant bacterium Acidiphilium utilized both organic and inorganic carbon, and obtained energy from organic matter, inorganic sulfur, and sunlight simultaneously. It was suggested that sunlight, rather than chemical energy of reduced iron-sulfur was the major driver of elemental cycling in the AMD lake. The results are beneficial to the development of bioremediation strategies for AMD.

Shipborne single-photon fluorescence oceanic lidar: instrumentation and inversion

Laser-induced fluorescence (LIF) technology has been widely applied in remote sensing of aquatic phytoplankton. However, due to the weak fluorescence signal induced by laser excitation and the significant attenuation of laser in water, profiling detection becomes challenging. Moreover, it remains difficult to simultaneously retrieve the attenuation coefficient (K l i d a r m f) and the fluorescence volume scattering function at 180° (βf) through a single fluorescence lidar. To address these issues, a novel all-fiber fluorescence oceanic lidar is proposed, characterized by: 1) obtaining subsurface fluorescence profiles using single-photon detection technology, and 2) introducing the Klett inversion method for fluorescence lidar to simultaneously retrieve K l i d a r m f and βf. According to theoretical analysis, the maximum relative error of βf for the chlorophyll concentration ranging from 0.01 mg/m3 to 10 mg/m3 within a water depth of 10 m is less than 20%, while the maximum relative error of K l i d a r m f is less than 10%. Finally, the shipborne single-photon fluorescence lidar was deployed on the experimental vessel for continuous experiments of over 9 hours at fixed stations in the offshore area, validating its profiling detection capability. These results demonstrate the potential of lidar in profiling detection of aquatic phytoplankton, providing support for studying the dynamic changes and environmental responses of subsurface phytoplankton.

Simultaneous sensing profiles of beam attenuation coefficient and volume scattering function at 180° using a single-photon underwater elastic-Raman lidar

Lidar has emerged as a promising technique for vertically profiling optical parameters in water. The application of single-photon technology has enabled the development of compact oceanic lidar systems, facilitating their deployment underwater. This is crucial for conducting ocean observations that are free from interference at the air-sea interface. However, simultaneous inversion of the volume scattering function at 180° at 532 nm (βm) and the lidar attenuation coefficient at 532 nm (K l i d a r m) from the elastic backscattered signals remains challenging, especially in the case of near-field signals affected by the geometric overlap factor (GOF). To address this challenge, this work proposes adding a Raman channel, obtaining Raman backscattered profiles using single-photon detection. By normalizing the elastic backscattered signals with the Raman signals, the sensitivity of the normalized signal to variations in the lidar attenuation coefficient is significantly reduced. This allows for the application of a perturbation method to invert βm and subsequently obtain the K l i d a r m. Moreover, the influence of GOF and fluctuations in laser power on the inversion can be reduced. To further improve the accuracy of the inversion algorithm for stratified water bodies, an iterative algorithm is proposed. Additionally, since the optical telescope of the lidar adopts a small aperture and narrow field of view design, K l i d a r m tends to the beam attenuation coefficient at 532 nm (cm). Using Monte Carlo simulation, a relationship between cm and K l i d a r m is established, allowing cm derivation from K l i d a r m. Finally, the feasibility of the algorithm is verified through inversion error analysis. The robustness of the lidar system and the effectiveness of the algorithm are validated through a preliminary experiment conducted in a water tank. These results demonstrate that the lidar can accurately profile optical parameters of water, contributing to the study of particulate organic carbon (POC) in the ocean.

Sensing profiles of the volume scattering function at 180° using a single-photon oceanic fluorescence lidar

A novel oceanic fluorescence lidar technique has been proposed and demonstrated for remotely sensing the volume scattering function at 180° (βf), which can be used to further retrieve the profiles of the absorption coefficient of phytoplankton (aph) at 532 nm and chlorophyll concentration (Chl). This scheme has these features. 1) The single-photon detection technology is employed to enhance the detection sensitivity to the single-photon level, enabling the oceanic lidar to obtain fluorescence backscatter profiles. 2) In terms of algorithms, the Raman backscattered signals of the water are utilized to normalize the backscattered signals of chlorophyll fluorescence, effectively minimizing the depth-dependent variation of the differential lidar attenuation coefficient (Δ K l i d a r f r). To reduce the contamination of fluorescence signals in the Raman backscatter signals, a Raman filter with a bandwidth of 6 nm was chosen. Subsequently, a perturbation method is utilized to invert the βf of the fluorescence lidar. Finally, aph and Chl profiles can be inverted based on empirical models. 3) The value of Δ K l i d a r f r used in inversion is obtained through a semi-analytic Monte Carlo simulation. According to theoretical analysis, the maximum relative error of βf for Chl ranging from 0.01 mg/m3 to 10 mg/m3 is less than 13 %. To validate this approach, a field experiment was conducted aboard the R/V Tan Kah Kee in the South China Sea from September 4th to September 5th, 2022, resulting in continuous subsurface profiles of βf, aph, and Chl. These measurements confirm the robustness and reliability of the oceanic single-photon fluorescence lidar system and the inversion algorithm.

Decadal evolution of an acidic pit lake: Insights into the biogeochemical impacts of microbial community succession

Acidic pit lakes represent hydrological features resulting from the accumulation of acid mine drainage in mining operations. Long-term monitoring is essential for these extreme and contaminated environments, yet tracking investigations integrating microbial geochemical dynamics in acidic pit lakes have been lacking thus far. This study integrated historical data with field sampling to track decadal biogeochemical changes in an acidic pit lake. With limited artificial disturbance, significant and sustained biogeochemical changes were observed over the past decade. Surface water pH slowly increased from 2.8 to a maximum of 3.6, with a corresponding increase in bottom water pH to around 3.9, despite the accumulation of externally imported sulfate and metals. Elevated nutrient levels stimulated the macroscopic growth of Chlorophyta, resulting in a shift from reddish-brown to green water with floating algal bodies. Furthermore, microalgae-fixed organic carbon promoted the transition from the initial chemolithotrophy-based population dominated by Acidiphilium and Ferrovum to a heterotrophic community. The increase in heterotrophic iron- and sulfate-reducers may cause an elevation in ferrous levels and a decline in copper concentrations. However, most metals were not removed from the water column, potentially due to insufficient biosulfidogenesis or sulfide reoxidation. These findings offer novel insights into microbial succession in extreme ecosystem evolution and contribute to the management and remediation of acidic pit lakes.

Sensing the profile of particulate beam attenuation coefficient through a single-photon oceanic Raman lidar

A lidar technique has been proposed and demonstrated for remotely sensing particulate beam attenuation coefficient (cp) profiles using the Raman backscattered signal from water. In Raman lidar, the backscatter coefficient at 180° can be considered constant, allowing for the determination of the lidar attenuation coefficient (Klidar) from the Raman backscattered signal. This scheme has these features. 1) The bandwidth of the filter that used to extract the Raman component from the backscattered signal of the lidar was optimized to ensure sufficient lidar signal strength while minimizing the influence of chlorophyll fluorescence on inversion. 2) A receiving telescope with narrow field of view (FOV) and small aperture was utilized to suppress multi-scattering components in the backscattered signal. 3) A relationship between the beam attenuation coefficient (c) and Klidar was established after simulations via a semi-analytic Monto Carlo. 4) The value of cp was obtained by subtracting the attenuation coefficient of pure seawater (cw) from c. According to the theoretical analysis, the maximum relative error of cp is less than 15% for chlorophyll concentrations up to 10 mg/m3. Due to the water Raman backscattered signal being several orders of magnitude lower than the elastic backscattered signal, a single-photon detector is required to significantly improve the detection sensitivity to the single-photon level. To validate this approach, a field experiment was conducted aboard the R/V Tan Kah Kee in the South China Sea from September 4th to September 5th, 2022, and continuous subsurface profiles of cp were obtained. These measurements confirm the robustness and reliability of the oceanic single-photon Raman lidar system and the inversion method.

Contrasting prokaryotic and eukaryotic community assembly and species coexistence in acid mine drainage-polluted waters

Acid mine drainage (AMD) is characterized by high acidity and high-concentration metals and sulfate, representing an extreme environment to life as well as environmental challenge worldwide. Microorganisms thriving in AMD habitats have evolved with distinct mechanisms in response to multiple stresses. Compared with microbial prokaryotes, our understanding regarding eukaryotic occurrence and role in AMD habitats remain limited. Here we examined microbial diversity and co-occurrence pattern within all domains of life in five lakes with varying degrees of AMD contamination ranging from extremely acidic to neutral. We demonstrated that AMD pollution reduced both eukaryotic and prokaryotic diversity in the lakes. In lakes with serious AMD pollution, chemoautotrophs including Ferrovum, Acidithiobacillus, and Leptospirillum showed significantly higher abundance, whereas with the macroscopic growths of photosynthetic microalgae (e.g., Coccomyxa and Chlamydomonas), heterotrophic or mixotrophic prokaryotes (e.g., Acidiphilium, Thiomonas, and Alicyclobacillus) increased in less polluted lakes. In the further improved ecosystems, Ochromonas, Rotifer, Ciliophora and other microeukaryotes appeared. Combined with a public dataset focusing on the microbes along an AMD-contaminated stream, we further demonstrated that acidity-dominated environmental selection served as the primary driver of both eukaryotic and prokaryotic community assemblies, and to a greater extent for eukaryotes. Furthermore, specific prokaryotic and eukaryotic taxa (e.g., Proteobacteria and Chlorophyta) exhibited wide taxonomic and functional associations in these AMD-polluted waters. These findings expand our knowledge on the eukaryotic diversity in AMD habitats, and provide insights into the ecological processes underlying microbial communities in response to AMD contamination.

Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake

Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.

Non-charismatic waterbodies and ecosystem disservices: Mine pit lakes are underrepresented in the literature

Pit lakes are one of the greatest legacies of open-cut mining. Despite the potential hazards of these lakes, they represent newly formed ecosystems with great scientific and ecological potential. Although thousands of pit lakes occur on every inhabited continent, with more being created, the microbial ecology of pit lakes is relatively under-researched. We evaluated the current state of microbial research in pit lakes by performing a Web of Science search and creating a literature database. Study lakes were categorized according to location and water quality (pH and conductivity) which is a key community and environmental concern. Research technology employed in the study was also categorized. We compared research effort in lakes, rivers, and streams which are the more "charismatic" inland aquatic ecosystems. Pit lake publications on microbes from 1987 to 2022 (n = 128) were underrepresented in the literature relative to rivers and streams (n = 321) and natural lakes (n = 948). Of the 128 pit lake publications, 28 were within the field of geochemistry using indirect measures of microbial activity. Most pit lake microbial research was conducted in a few acidic lakes in Germany due to social pressure for remediation and government initiative. Relatively few studies have capitalized on emerging technology. Pit lake microbial research likely lags other more charismatic ecosystems given that they are viewed as performing "ecosystem disservices," but this is socially complex and requires further research. Improving understanding of microbial dynamics in pit lakes will allow scientists to deliver safer pit lakes to communities.

Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake

Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.

Gas Pressure Dynamics in Small and Mid-Size Lakes

Dissolved gases produce a gas pressure. This gas pressure is the appropriate physical quantity for judging the possibility of bubble formation and hence it is central for understanding exchange of climate-relevant gases between (limnic) water and the atmosphere. The contribution of ebullition has widely been neglected in numerical simulations. We present measurements from six lacustrine waterbodies in Central Germany: including a natural lake, a drinking water reservoir, a mine pit lake, a sand excavation lake, a flooded quarry, and a small flooded lignite opencast, which has been heavily polluted. Seasonal changes of oxygen and temperature are complemented by numerical simulations of nitrogen and calculations of vapor pressure to quantify the contributions and their dynamics in lacustrine waters. In addition, accumulation of gases in monimolimnetic waters is demonstrated. We sum the partial pressures of the gases to yield a quantitative value for total gas pressure to reason which processes can force ebullition at which locations. In conclusion, only a small number of gases contribute decisively to gas pressure and hence can be crucial for bubble formation.