Anne D. Jungblut

One hundred diatom species have been selected for genome and transcriptome sequencing. The 100 Diatom Genomes Project aims to provide a scalable framework for understanding diatom biodiversity, ecology and evolution, and for investigating their use in biotechnology.

Perennially ice-covered lakes are hotspots of biodiversity and biomass accumulation in polar deserts. Many Antarctic perennially ice-covered lakes are density stratified, within which an oxygenated upper layer overlies deeper, darker anoxic waters. We carried out the first 16S and 18S rRNA gene high throughput sequencing of microplankton and benthic microbial mats in perennially ice-covered Lake Joyce, McMurdo Dry Valleys, Antarctica. We evaluated community composition and richness at different lake and water depths, and determined the level of connectivity of benthic and planktonic microbial communities. While some overlap between benthos and plankton was observed, the microbial communities were distinct in richness and community composition. The benthic communities comprised microbial mats, which were dominated by Cyanobacteria and Proteobacteria, whereas the planktonic community showed an increased contribution of Bacteroidota. A higher number of 16S rRNA gene ASVs were specific for the plankton than the mats, whereas more 18S rRNA gene ASVs were specific to the microbial mats than the plankton. The benthic eukaryotic community was dominated by ciliates and diatoms while Cryptophyceae were abundant in the plankton. These findings demonstrate that both benthic and planktonic communities need to be considered for census of taxonomic richness, productivity, and ecological processes occurring within Antarctic lakes.

Climate warming threatens Arctic permafrost with seasonal cycles of freezing and thawing. Arctic soil microorganisms regulate carbon stocks and greenhouse gas exchanges with the atmosphere, yet their precise seasonal growth and dormancy dynamics, and their responses to permafrost thaw, are not well understood. We thawed frozen Svalbard active layer soil and traced microbial growth using DNA quantitative stable isotope probing with H ₂ ¹⁸ O. We observed temporal growth patterns resulting in distinct early (21-day) and late-stage (98-day) growing microbial populations. In particular, Acidobacteriota, Actinobacteriota, Bacteroidota, Proteobacteria, and predatory and epibiont bacterial taxa (such as those affiliated to Bdellovibrionota and Patescibacteria) were identified in the soil active layer as clades that were growing following thawing. Methane concentrations in our microcosms remained low, yet pmoA genes were ¹⁸ O-labeled, indicating growth of aerobic methane-oxidizing bacteria. Approximately half of the microbial taxa detected did not grow, suggesting that Arctic soils constitute sizeable reservoirs of dormant microorganisms. Our results reveal complex and temporal microbial dormancy, growth, death, predation, and parasitism dynamics in seasonally changing Arctic soils. These processes likely regulate the exchange and storage of soil carbon across the increasingly vulnerable Arctic region. IMPORTANCE: Microorganisms play key roles in transforming soil carbon into greenhouse gases. As Arctic soils warm as a result of climate change, greater depths and expanses of permanently frozen soil are experiencing seasonal thaw. Despite the importance of active soil microorganisms in transforming soil carbon, the seasonal freezing and thawing of Arctic soils and associated dormancy and re-activation of microbial populations are not well constrained. Here, we thawed and incubated active layer (i.e., seasonally thawing) Arctic soil with a stable isotope to directly label the DNA of growing soil microorganisms. We found that half of the microbial diversity did not grow after thaw and that some groups, including the Bacteroidota and predatory bacteria, grew disproportionately. The growing microbial community shifted over time, and bacteria capable of oxidizing methane grew more after prolonged thaw. These findings highlight that dormancy, predation, and variable growth dynamics are important factors determining ecological and biogeochemical processes in thawing Arctic soil.

Arctic freshwater biodiversity is rapidly changing due to climate warming, resource extraction, infrastructure development, and landscape transformation. To improve understanding, predict future responses, and inform policy formulation, research needs must be clearly identified. Using a horizon scan survey, Arctic freshwater experts from government, international agencies, and Indigenous Peoples identified 77 biodiversity research questions with 17 highlighted as most important for near term assessment. These questions span nine thematic categories: biodiversity and taxonomic challenges, hydrological change, productivity and food webs, ecosystem connectivity, methods, monitoring and assessment, permafrost change, winter ecology, anthropogenic development, and Indigenous Knowledge. Climate change emerged as the major driver among all categories and research questions. A key priority identified was the urgent need for long-term, harmonized monitoring programs among Arctic countries. Multiple knowledge gaps detected suggest that circumpolar research collaborations are required to tackle these issues.

Acid mine drainage (AMD) is an environmental concern that needs to be addressed by some mining industries because of its high concentrations of metals and acidity that destroy affected ecosystems. Its formation typically persists beyond the operating life of a mine site. Its management is even more challenging for sites that are abandoned without rehabilitation. In this study, a legacy copper–gold mine located in Sto. Niño, Tublay, Benguet, Philippines, generating a copper- and manganese-rich AMD (Cu, maximum 17.2 mg/L; Mn, maximum 2.90 mg/L) at pH 4.59 (minimum) was investigated. With its remote location inhabited by the indigenous people local community (IPLC), a novel limestone-based hybrid passive treatment system that combines a limestone leach bed (LLB) and a controlled modular packed bed reactor (CMPB) has been developed from the laboratory and successfully deployed in the field while investigating the effective hydraulic retention time (HRT), particle size, and redox conditions (oxic and anoxic) in removing Cu and Mn and increasing pH. Laboratory-scale and pilot-scale systems using simulated and actual AMD, respectively, revealed that a 15 h HRT and both oxic and anoxic conditions were effective in treating the AMD. Considering these results and unsteady conditions of the stream in the legacy mine, a hybrid multi-stage limestone leach bed and packed bed were deployed having variable particle size (5 mm to 100 mm) and HRT. Regular monitoring of the system showed the effective removal of Cu (88.5%) and Mn (66.83%) as well as the increase of pH (6.26), addressing the threat of AMD in the area. Improvement of the lifespan of the system needs to be addressed, as issues of Cu-armoring were observed, resulting in reduced performance over time. Nonetheless, the study presents a novel technique in implementing passive treatment systems beyond the typical treatment trains reported in the literature.

Traditional medicinal knowledge remains an important source of healthcare for many communities in the Philippines, particularly in rural and Indigenous areas where access to modern treatments is limited. In this context, Vaccinium uliginosum (locally known as Ayusip), a plant used by indigenous peoples in Tublay, Benguet Province, has drawn interest due to its reported therapeutic applications for ailments such as cough, flu, and even cancer. This study investigates the cytotoxic properties of Ayusip, aiming to provide scientific validation for its traditional use and assess its potential as a source of bioactive compounds for cancer treatment. Leaves of V. uliginosum were collected, identified, and subjected to methanol extraction, with further partitioning using n-hexane and ethyl acetate. Phytochemical analysis indicated high levels of flavonoids, saponins, steroids, and tannins. Quantification showed significant phenolic (24.58±8.11 GAE mg/g) and flavonoid (121.38±14.04 QE mg/g) content. Antioxidant testing (DPPH assay) revealed strong activity (97.86±1.33%) at 25 mg/mL. The cytotoxicity of V. uliginosum was assessed against normal embryonic lung fibroblasts (MRC-5) and cancer cell lines HCT-116 (colorectal) and A549 (lung adenocarcinoma) using the MTT assay. Results showed that only the n-hexane extract was toxic to MRC-5 cells at high concentrations, while methanol and n-hexane extracts were highly cytotoxic to HCT-116 cells. In A549 cells, only n-hexane extract exhibited cytotoxicity. These findings suggest that V. uliginosum has promising cytotoxic effects, particularly at higher concentrations, with notable activity against HCT-116 cells. Interestingly, its cytotoxicity is biphasic: high concentrations induce maximum toxicity, whereas lower concentrations may encourage cell proliferation. Overall, this study offers insights into the cytotoxic potential of V. uliginosum, a traditionally used plant among Benguet’s IPs, highlighting its potential medicinal value.

Multiple names are used to describe the same group of root-associated fungi. Following the International Conference for Mycorrhizas 12, we propose unifying them as ‘ֹMFRE’ to improve clarity and consistency and distinguish them from similar groups.

Background: Self-organizing maps (SOMs) are a class of neural network algorithms able to visually describe a high-dimensional dataset onto a two-dimensional grid. SOMs were explored to classify soils based on an array of physical, chemical, and biological parameters. Methods: The SOM analysis was performed considering soil physical, chemical, and microbial data gathered from an array of apple orchards and strawberry plantations managed by organic or conventional methods and located in different European climatic zones. Results: The SOM analysis considering the “climatic zone” categorical variables was able to discriminate the samples from the three zones for both crops. The zones were associated with different soil textures and chemical characteristics, and for both crops, the Continental zone was associated with microbial parameters—including biodiversity indices derived from the NGS data analysis. However, the SOM analysis based on the “management method” categorical variables was not able to discriminate the soils between organic and integrated management. Conclusions: This study allowed for the discrimination of soils of medium- and long-term fruit crops based on their pedo-climatic characteristics and associating these characteristics to some indicators of the soil biome, pointing to the possibility of better understanding the interactions among diverse variables, which could support unraveling the intricate web of relationships that define soil quality.

This study developed a system intended to treat a copper-rich acid mine drainage (AMD) in a legacy mine in Sto. Niño, Tublay, Benguet, Philippines. Based on previous sampling campaigns in the area, Cu and Mn concentrations and pH exceed the local effluent standards. Using local limestone as the media for treatment of AMD, several laboratory experiments using synthetic AMD were conducted to identify the effective particle size and hydraulic retention time. Consequently, the parameters identified were then deployed into a pilot-scale system investigating the effectiveness of an oxic and anoxic system for the actual AMD. Conducting the analysis, it has revealed that a hybrid of oxic and anoxic system with variable particle size and hydraulic retention time may be deployed considering the unsteady condition of the stream in the legacy mine. In Consideration of the topography of the mine site, a hybrid multi-stage limestone leach bed and packed bed has been deployed. With regular monitoring of the system, it showed an effective removal of Cu and Mn and increase pH of the stream. This observation thus addresses the threat of AMD in the area. However, improvement in terms of the lifespan of the system needs to be demonstrated as common issues of armoring from high concentration of Cu is observed resulting in the reduction of treatment performance over time.