Exploring the Distribution and Biodiversity of microbial RuBisCO  in Natural Environments via Genome Database

摘要：

RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is the most abundant enzyme in nature, responsible for fixing CO2 in the Calvin-Benson-Bassham (CBB) cycle, playing a crucial role in the carbon entry into the biosphere and the process of photosynthesis. It is found in most autotrophic organisms, including bacteria, archaea, and eukaryotes (algae and higher plants). RuBisCO is distributed across different ecosystems, from land to oceans, and its ability to capture and fix CO2 directly affects global carbon cycles including the soil organic carbon (SOC) storage. 

    We identified 9,805 genomes (70% are metagenomes) carrying RuBisCO from 85,205 genome database, and we collected their natural environments data from by manually from GTDB, BacDive, NCBI BioSample database. We use the IQ-TREE tool to reconstruct phylogenetic tree of RuBisCO protein sequences, to reveal the evolution and distribution of RuBisCO across various CO2 fixing microorganisms. Moreover, we map their natural environments onto phylogenetic tree. Our data showed that 49.73% of RuBisCO carry species are Proteobacteria, 14.09% is Cyanobacteria,7.60% is Actinobacteria,7.21% is Firmicutes and 1.72% is Euryarechaeota and Bacteroidotes. Based on multiple data analysis, we reveal the distribution and biodiversity of microbial RuBisCO in different natural environments. We also identified the RuBisCO-carrying species in the soil to show the potential producers of soil carbon sinks (SOC). Our result suggests that those CO2 fixing microorganisms (including uncultured species) using RuBisCO protein in different environments have important impacts on various ecosystems on Earth.

Changes in the gut microbiota of white shrimp infected with Vibrio parahaemolyticus after feeding Bacillus pumilus probiotics at different stocking densities

摘要：

As global demand for aquatic products grows, intensive aquaculture has led to disease outbreaks and pollution. White shrimp (Litopenaeus vannamei), accounting for half of global crustacean aquaculture, faces economic losses from Acute Hepatopancreatic Necrosis Disease (AHPND) caused by Vibrio parahaemolyticus. Without an adaptive immune system, shrimp rely on balanced gut microbiota for health. Antibiotics cause residues and pollution, making probiotics a sustainable alternative. High-density farming, now unavoidable, increases stress, disrupts gut microbiota, and raises disease risks, highlighting the need to study probiotics under varying densities.

This study aims to investigate on the gut microbiota of white shrimp, focusing on its impact on key bacterial taxa such as Vibrio and Bacillus species. It also compares the effects of Bacillus pumilus D5 probiotics against Vibrio parahaemolyticus at different stocking densities. Two densities, low (100 shrimp/m²) and high (200 shrimp/m²), were tested with (+B) and without (-B) probiotics, resulting in four groups: LD+B, LD-B, HD+B, and HD-B .Each condition has two replicates, totaling eight tanks. Shrimp were fed probiotic-enriched feed (10⁷ CFU/g) for two weeks before being challenged with V. parahaemolyticus. Samples were collected at 0, 6, 12, and 24 hours post-infection.

Expected qPCR analysis results indicate that virulence gene expression in probiotic-treated groups (LD+B and HD+B) will decrease due to the ability of probiotics to inhibit pathogenic bacteria. Regarding gut microbiota composition, probiotic-treated groups are anticipated to exhibit a lower relative abundance of Vibrio species, while untreated groups (LD-B and HD-B), especially under high-density conditions, are likely to show higher Vibrio levels due to density-induced stress. Conversely, probiotic-treated groups are expected to exhibit a higher relative abundance of Bacillus species, while untreated groups are likely to show lower levels.

Investigating the influence of tomato SWEET3 transporter on the rhizosphere microbiota and its relationship with Bacillus subtilis

摘要：

This study investigates the role of the tomato SWEET3 (Sugar Will Eventually Be Exported Transporter 3) gene in shaping the rhizosphere microbiota and its interactions with Bacillus subtilis. SWEET3 primarily releases glucose into the rhizosphere, providing a carbon source that influences microbial abundance and composition. While previous studies show SWEET3 affects B. subtilis colonization, its impact on overall rhizosphere microbiota structure and microbial interactions remains unclear.

To explore this, we used three tomato genotypes: the control group (Control), SWEET3 overexpression line (OE), and knockout line (KO). A strain of B. subtilis was introduced to observe its colonization and performance differences among genotypes. We hypothesize that SWEET3 overexpression enhances glucose release, promoting B. subtilis colonization and increasing rhizosphere microbial abundance and diversity. Conversely, knockout plants with reduced glucose release may inhibit B. subtilis colonization, leading to a decrease in microbial diversity and abundance.

This study addresses two key questions: (1) Does SWEET3 alter the abundance and composition of the rhizosphere microbiota? (2) How do changes in carbon supply by SWEET3 affect B. subtilis colonization, biofilm formation, and interactions with other rhizosphere microbes? By exploring these relationships, we aim to provide insights into how plants regulate the rhizosphere ecosystem through carbon supply, supporting biological control strategies and plant health management.

Investigating Environmental Drivers of Microbial Community Dynamics and Their Impact on Oyster Farming Sustainability Along the Southwest Coast of Taiwan

摘要：

The southwest coast of Taiwan is a key region for oyster farming, but faces significant challenges from climate change, pollution, and harmful algal blooms (HABs) such as green and red tides. Previous studies have usually focused on one farm site, with a lack of data at the regional level.

To address this, we collected samples from eight sites in four major oyster farming counties of Taiwan: Changhua (Fubao, Wanggong), Yunlin (Taixi, Kouhu), Chiayi (Dongshi, Budai), and Tainan (Luzhugou, Qigu). This study investigates the microbial communities in seawater from oyster farms and their correlations with nutrient and metal levels, as well as weather factors.

Biweekly sampling included seawater filtration, DNA extraction, and sequencing to analyze the diversity and composition of microbial communities. Environmental data such as temperature and pH were recorded in the field, and nutrient and metal concentrations were measured in the laboratory.

This study aims to determine (1) the spatial and temporal dynamics of microbial communities in oyster farming ecosystems, (2) which environmental factors are significantly correlated with microbial diversity and composition, (3) whether the changes in environmental factors and microbial communities are associated with local oyster production. This research aims to improve the understanding of the underlying abiotic and biotic effects that influence the sustainability of oyster aquaculture.

Effects of spraying probiotic Bacillus subtilis on the tomato phyllosphere microbiota and disease resistance to Pseudomonas syringae

摘要：

The leaf environment is complex and highly susceptible to pathogen invasion, making the ability to resist biotic stress crucial. The phyllosphere microbiota plays an essential role in enhancing leaf resistance by competing with pathogens for ecological niches and secreting antimicrobial substances to form protective barriers against pathogen infection. This study designed four experimental groups (control, Bacillus subtilis only, Pseudomonas syringae pv. tomato only, and Bacillus subtilis followed by Pseudomonas syringae pv. tomato) to simulate microbial dynamics under different treatments. The results showed that Pseudomonas syringae pv. tomato infection significantly reduced the diversity of the phyllosphere microbiota. However, spraying Bacillus subtilis 6 hours prior to pathogen inoculation partially restored the diversity of the phyllosphere microbial community. Nonetheless, pre-spraying Bacillus subtilis had limited effects on colonization on the leaf surface and suppressing disease caused by Pst DC3000. Furthermore, the study revealed that Bacillus subtilis significantly altered the structure of microbial communities in infected leaves. Future research will focus on dual-culture assays and 16S rRNA gene sequencing to further investigate the impact of Bacillus subtilis on the overall structure of the phyllosphere microbiota, elucidating its ecological roles and its effectiveness in enhancing tomato disease resistance.

Keywords: Phyllosphere Microbiota, Bacillus subtilis, Pseudomonas syringae pv. Tomato, Biocontrol Agent, Disease Resistance

Dynamic changes of the anaerobic microbial community in a methane-producing system under high salinity stress.

摘要：

With increasing organic wastewater discharge, anaerobic digestion (AD) is an efficient, sustainable treatment method. AD relies on three key microbial groups: fermentative bacteria convert complex organic compounds into volatile fatty acids (VFAs); syntrophic bacteria transform VFAs into acetate and hydrogen; methanogenic archaea produce methane. High salinity in organic wastewater inhibits microbial activity, challenging AD efficiency, particularly for methanogens and syntrophic bacteria. Enhancing their salt tolerance and understanding their response mechanisms is essential for improving AD under high-salinity conditions. This study explores structural and functional changes in AD microbial communities under dynamic salinity stress, focusing on methanogens, syntrophic bacteria, and their salt tolerance thresholds. Simulated conditions increased salinity to 4% across reactors: control (D1), salinity (D2, D3), and salinity with aspartic acid (D4). Multi-level analyses used 16S rDNA time-series and RNA-Seq. Core salt-tolerant groups were identified, and aspartic acid’s role as an osmoprotectant was evaluated.

At 3.2% salinity, system performance—COD removal and methane production—declined significantly, alongside drastic microbial shifts. Diversity analyses revealed strong environmental filtering, reducing diversity and altering community structure. The aspartic acid group (D4) maintained higher stability under high salinity, increasing Methanosarcina abundance. Methanosarcina and Methanobacterium dominated methanogens, while Smithella led the syntrophic stage. RNA-Seq revealed that aspartic acid upregulated the ablA gene, enhancing Methanosarcina’s osmoregulation. D4 also showed higher expression of Nε-Acetyl-β-Lysine pathway genes, mitigating salinity’s inhibitory effects. This study highlights salt-tolerant taxa and demonstrates aspartic acid’s potential to stabilize AD systems, offering insights for addressing salinity stress in wastewater treatment.

台灣大學葉宇晨

Disentangling the biogeography and local adaptation of Saccharomycotina yeasts

摘要: 

Broadleaf Fagaceae forests in East Asia are one of the geographical origins of the baker’s yeast Saccharomyces cerevisiae that harbor genetically divergent lineages. Investigations of environmental factors contributing to the evolution and adaptation of S. cerevisiae or other yeasts in nature are currently emerging. This project aims to infer the evolutionary history of multiple yeast species in East Asia through comparative population genomics approaches.

We preliminary quantified inter- and intra-genetic diversities in a total of 518 S. cerevisiae, 29 S. kudriavzevii, and 171 Lachancea thermotolerans strains, of which 174 were genome-sequenced and collected from East/Southeast Asian countries including Taiwan, Vietnam and the Philippines. Phylogenetic trees inferred from single nucleotide polymorphisms and concatenated single-copy orthologues revealed basal lineages for all species tested are preserved in Taiwan. The most divergent lineage identified from our sampling of L. thermotolerans showed genetic differentiation index Fst between 0.81 and 0.89 against other subpopulations. In addition to the high nucleotide diversity from wild populations, the results supported that some non-Saccharomyces yeasts also originated from East Asian regions. As we hypothesized yeast populations continued to diversify after dispersal to different regions, future work includes quantifying the extent of repeated local adaptations amongst strains.

Characterization of rice root and soil microbiota in paddy fields subjected to conventional and organic management

摘要：

Microbes can have a significant impact on crops. They can affect plant biology directly through roots or indirectly through soil. In this study, we characterized the soil (surface or deep) and root bacterial community compositions, in 9 local paddy fields (6 under conventional and 3 under organic management),  during the spring cropping season in 2024. A total of 74 samples were analyzed for 16S rDNA-based bacterial compositions. Shannon index and Chao 1 index were not significantly affected by sample type, management, sampling site, or developmental stage (Kruskal-Wallis rank sum test, p > 0.05). PERMANOVA results show that sample type, field management, plant development, and sampling site have significant effects on microbial composition (p < 0.02). We observed a deep soil-surface soil-root (DSR) gradient along the first NMDS axis and progressing developmental stages along the second NMDS axis. The majority (n=76) of the 100 most abundant genus-level taxa have no formally established genus names. Among the dominant genera, 55 and 45 dominant genera have positive and negative correlations with plant development (Spearman’s correlation, p < 0.05). There are 26 and 44 have positive and negative correlations with the DSR gradient (Spearman’s correlation, p < 0.05). Potential nitrogen fixing taxa Allorhizobium -Neorhizobium -Pararhizobium -Rhizobium has positive correlations with the DSR gradient in both conventional and organic fields, but for Bradyrhizobium the positive correlation was only seen in the organic field. The most dominant genus, Bacillus, shows a positive correlation in root but a negative correlation in surface soil with plant development. It also shows a negative correlation with DSR in conventional fields but not so in the organic fields.

中山大學 廖祥佑      

Microbial Community Composition of Anthopleura in the Hydrothermal Environments of Kueishantau(Turtle Island)

摘要

The shallow hydrothermal vents around Kueishantau(Turtle Island), located off the northeastern coast of Taiwan, represent one of the most unique marine ecosystems in the region. These vents discharge highly acidic (pH 1.75–4.60), sulfur-rich fluids with temperatures ranging from 65°C to 116°C, creating localized conditions with low pH (5.4–7.3) and reduced dissolved oxygen (DO) compared to normal seawater (Jeng et al., 2004; Chiu et al., 2022). These extreme conditions, characterized by high temperatures and high concentrations of sulfides and other toxic chemicals, are lethal to most organisms. Despite these harsh conditions, certain species have evolved to thrive in such environments. A species of sea anemone, Anthopleura, has been discovered near these vents, exhibiting remarkable adaptations that allow it to survive in this extreme habitat. It is hypothesized that Anthopleura employs unique adaptive mechanisms, including physiological, molecular, and symbiotic microbiome-level regulations, enabling it to tolerate high temperatures, toxic chemicals (such as sulfides and metals), and low oxygen conditions. In this study, we aim to investigate the adaptive mechanisms of Anthopleura in extreme environments through symbiotic microbiome analyses and aquarium-based experiments, providing valuable insights into the ecological dynamics and survival strategies in hydrothermal vent ecosystems.

Defining species boundaries in bacteria: No universal threshold based on genome-wide average nucleotide identity (ANI)

摘要：

The definition of species is a fundamental question in biology. To define bacterial species, genome-wide average nucleotide identity (ANI) is commonly used. One large-scale study in 2018 using ~90,000 prokaryotic genomes revealed a bimodal distribution of ANI values, with within-species comparisons mostly resulted in > 95% ANI, while between-species comparisons mostly resulted in < 83% ANI. Based on that study, a threshold of 95% ANI has been generally accepted for classifying strains to species. However, this threshold has been challenged, and the lack of consideration for the alignment fraction (AF; the proportion of genome sequences used for calculating ANI) represents another issue. For a more in-depth investigation into this topic, we selected 18 important bacterial genera for analysis. After quality control and de-replication, a total of 25,879 genome sequences were used. Our results demonstrated that the distribution pattern of ANI values varied considerably among these genera. While in some groups (e.g., Agrobacterium, Legionella, Chlamydia) the discrete distribution of ANI values suggested the existence of clear threshold for defining species boundaries, in some other groups (e.g., Streptococcus, Bacillus, Pseudomonas) the ANI values exhibited a continuous distribution, making the species delineation difficult. These findings suggested that no universal threshold exist for delineating species across different bacteria based on only ANI values. Although when AF and ANI values are considered jointly, a better resolution can be achieved, for groups that have large numbers of genome sequences available (e.g., Bacillus with 3,102 assemblies and Pseudomonas with 5,120 assemblies), species delineation based on ANI and AF values remain difficult. Taken together, our results highlight the complexity involved in delineating species. While the popular 95% ANI threshold provides a quick and easy method for species assignment, such approach should be used with caution. For robust taxonomy, more detailed analysis such as core-genome phylogeny and gene content comparison, as well as polyphasic approaches that consider phenotype are important.

Enhancing Crop Growth and Soil Fertility in Taiwan's Badlands with Green Manure and PGPR

摘要：

Southern Taiwan contains extensive terrains known for its challenging landscapes, often referred to as "badlands". These areas are characterized by soils with high clay content, which hinders water infiltration and results in poor water retention, thereby constraining agricultural productivity. The incorporation of green manure, particularly legumes, has been shown to improve soil health by supplying organic matter, essential nutrients, and nitrogen through the activity of nitrogen-fixing bacteria in root nodules. This study investigates organic agricultural practices, including the use of green manure and plant growth-promoting rhizobacteria (PGPR), to ameliorate the conditions of badland soils and support crop growth. Preliminary results indicate that sunn hemp adapts well to these challenging soils, with PGPR further enhancing its growth. The initial data collection has indicated that the soil texture in the radish cultivation area is categorized as silty loam, exhibiting a slightly acidic pH level. The organic nitrogen and carbon content within the soil are approximately 0.1% and 0.8%, respectively. In the near future, a field experiment will be conducted to integrate green manure into the radish cultivation process, with the objective of improving agricultural productivity and promoting sustainability.

Isolation of DEHP-Degrading Microorganisms and Microbiota Composition Analysis in Japanese Eel

摘要：

The Japanese eel (Anguilla japonica) is endangered due to environmental pollution and overfishing. In Taiwan, wild populations are predominantly female, while aquaculture populations are mostly male, for reasons that remain unknown. Di (2-ethylhexyl) phthalate (DEHP), a prevalent phthalate ester and endocrine-disrupting chemical, accumulates in aquatic environments and causes reproductive toxicity in fish, but its effects on Japanese eels remain unexplored. We hypothesize that DEHP exposure contributes to female-biased sex ratios in wild eel populations by affecting sex differentiation and microbiota composition. This study will employ multi-omics analyses, including culturomics to isolate DEHP-degrading bacteria from eel gut and skin. Moreover, both microbiota compositional changes during glass eel development (0-7 months) and sex-determination gene expression will be examined to disclose the role of DEHP in female predominance in wild populations.

Identification of specific sex hormones and elucidation of the roles of gonad microbiota in the reproduction of Exaiptasia pallida

摘要：

Exaiptasia pallida, a sea anemone, serves as an important model organism in marine biology due to its rapid reproduction, remarkable adaptability, and transparent tissues, which facilitate observation and analysis. However, its reproductive mechanisms and the role of associated gonad microbiota remain unclear. This study aimed to identify specific sex hormones in E. pallida and investigated the role of its gonad microbiota in the reproduction cycle. We dissected the E. pallida weekly, and it was revealed that gonadal maturation was associated with the lunar cycle. Histological staining was employed to confirm sexual determination and developmental stages, while PacBio full-Length 16S rRNA gene amplicon Sequencing was used to analyze the gonadal bacterial community structure. It was shown that the associated bacterial composition was related to the sex of E. pallida, and there were specific bacteria in male gonad being capable of metabolizing androgens. Furthermore, lipidomic analysis exhibited potential androgen signals in the E. pallida extracts. ELISA and Yeast assays will be used to validate hormone activity, which could provide new insights into the reproductive mechanisms of E. pallida and the functional interactions between gonad microbiota and sex hormones.

高屏溪流域有機碳來源及微生物分解作用的時空變化

摘要：

河流微生物透過分解有機碳獲取能量，對碳的生物地球化學循環、營養鹽轉化及能量傳遞具有重要作用。有機碳來源多樣，包括陸源輸入及水體初級生產力，可能導致微生物功能在空間上的差異。研究指出，微生物主要由上游土壤經降雨和逕流進入河流，隨水流向下游遷移至河口。在季風氣候區，降雨模式的季節性變化顯著影響有機碳輸送及微生物代謝活性，但相關研究有限。本研究以高屏溪流域為研究地點，該流域屬荒溪型河流系統，其有機碳來源受到時空分布影響。水文特徵可能造成有機碳輸送的季節性差異，進而影響微生物群落的代謝模式。此外，高屏溪流域橫跨不同地形及土地利用型態，可能使微生物群落呈現空間異質性。本研究利用Ecoplate 生化代謝微孔盤對流域中三個支流和出海口共9個地點的河水及沉積物微生物群落進行培養，探討空間分布與季節變化對微生物群落使用不同有機碳源代謝活性的影響。結果顯示，沉積物微生物群落的代謝模式與河水微生物群落不同，主成分分析顯示沉積物微生物代謝活性在高低水位間差異顯著，七月沉積物樣本的可利用碳源數量最高，反映季節變化對沉積物代謝功能的重要影響。相比之下，河水微生物受到季節影響較小，但低水位時可利用碳源數量隨地點向下游增加，顯示空間異質性可能影響河水微生物的代謝功能。這些發現深化了對河流微生物功能多樣性的理解，也為未來評估氣候變遷對河流生態系統的影響提供重要基礎。

Anammox bacteria regulate organotrophic activity in response to osmotic stress

摘要：

Anaerobic ammonium-oxidizing (anammox) bacteria, previously thought to be strictly chemolithoautotrophy, exhibit a mixotrophic lifestyle. This mixotrophy, particularly chemoorganotrophy, is assumed to provide additional advantages by generating extra reducing equivalents and metabolite precursors under energy-deficient stress conditions. In this study, anammox bacteria closely related to Candidatus Brocadia sapporoensis were enriched and explored using a metagenomic approach. Ca. Brocadia sapporoensis genome exhibits complete central carbon metabolism pathways with key organotrophic genes. These include AMP-forming acetyl-CoA synthetase (acs gene) and various genes encoding nitrate and nitrite reductases that facilitate dissimilatory nitrate reduction to ammonium (DNRA). We systematically evaluated how Ca. Brocadia sapporoensis regulates organotrophic activity in response to increased salinity in the presence of acetate through batch assays and reactor operation. The batch assay results demonstrated that osmotic stress (2% salinity) and acetate as an electron donor significantly enhanced the nitrate reduction rate and the acs gene expression in Ca. Brocadia sapporoensis compared to freshwater conditions. During reactor operation, the transcriptional activities of genes involved in the tricarboxylic acid (TCA) cycle in Ca. Brocadia sapporoensis were significantly upregulated with acetate and 1% salinity. These findings suggest that Ca. Brocadia sapporoensis can metabolize acetate to enhance the DNRA activity, thereby facilitating the anammox process. Additionally, the acetyl-CoA synthesis from acetate further supports the TCA cycle for osmolyte synthesis and energy generation, helping Ca. Brocadia sapporoensis copes with high osmotic pressure. This study expands our understanding of the organotrophic activity and the osmoadaptation in Ca. Brocadia sapporoensis, providing valuable insights for optimizing the anammox process in treating organic-rich saline wastewater.

生物炭循環農耕應用於文旦園中影響的氮循環相關土壤微生物相 

摘要：

台灣預期於 2050 年達成淨零排放，意即以負碳技術、碳匯等方法抵消人為造成的溫室氣體排放。海洋藍碳、森林綠碳和土壤黃碳是三大碳匯策略，而生物炭的長半衰期可以使碳封存在土壤中，且隨著時間推移沉至地底，有助碳匯，成為黃碳裡一種熱門且常見的應對。生物炭的大表面積、多官能基和多孔隙可以使土壤通氣、為微生物提供棲地，藉此改良土壤性質、微生物菌相、增加植物抗性、促進生長和增進產量，其理化和微生物特性也影響溫室氣體減排。 

        文旦是台南重要經濟作物，而其大量的修剪枝去化是棘手的問題。利用循環農業，以文旦枝製備生物炭再施作於文旦園，既可以再利用農業剩餘資材，又可達成淨零目標，也能促進農民果實品質效益，是一舉數得的多贏局面。在此研究中，我們注重果園在施生物炭下對土壤的影響，包含理化性質和微生物性質，並且確認在施炭同時，不會降低果實品質和產量。

Aromatase-independent estrogenesis: Wood-Ljungdahl pathway likely contributed to the emergence of estrogens in the biosphere

摘要：

Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O2-dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the discovery of anaerobic estrogenesis in a Peptococcaceae bacterium (strain TUW77) isolated from the gut of the great blue-spotted mudskipper (Boleophthalmus pectinirostris). This strain exhibits unprecedented testosterone fermentation pathways, transforming testosterone into estrogens and androstanediol under anaerobic conditions. Physiological experiments revealed that strain TUW77 grows exclusively on testosterone, utilizing the androgenic C-19 methyl group as both the carbon source and electron donor. The genomic analysis identified three copies of a polycistronic gene cluster, abeABC (anaerobic bacterial estrogenesis), encoding components of a classic cobalamin-dependent methyltransferase system. These genes, highly expressed under testosterone-fed conditions, show up to 57% protein identity to the characterized EmtAB from denitrifying Denitratisoma spp., known for methylating estrogen into androgen (the reverse reaction). Tiered transcriptomic and proteomic analyses suggest that the removed C-19 methyl group is completely oxidized to CO2 via the oxidative Wood-Ljungdahl pathway, while the reducing equivalents (NADH) fully reduce remaining testosterone to androstanediol. Consistently, the addition of anthraquinone-2,6-disulfonate, an extracellular electron acceptor, to testosterone-fed TUW77 cultures enabled complete testosterone conversion into estrogen without androstanediol accumulation (anaerobic testosterone oxidation). This discovery of aromatase-independent estrogenesis in anaerobic bacteria suggests that the ancient Wood-Ljungdahl pathway may have contributed to the emergence of estrogens in the early biosphere.

FRCI: a sequence-based method to identify cyanobacteria that can grow in far-red light

摘要：

Cyanobacteria typically use visible light (VL; 𝜆 = 400-700 nm) for photosynthesis, but some also utilize far-red light (FRL; 𝜆 = 700-800 nm). These far-red light-utilizing cyanobacteria (FRLCyano) produce chlorophylls d or f in response to FRL and play crucial roles as primary producers in environments with limited VL. However, widely used pigment-based methods can only detect FRLCyano that have acclimated to FRL and cannot resolve the diversity of FRLCyano. Here, we develop a new method, Far-Red Cyanobacteria Identification (FRCI), using 16S rRNA gene sequences to identify FRLCyano. To test FRCI experimentally, we collected environmental samples and cultured them in VL and FRL to create microbial communities with a series of FRLCyano abundance levels. We found that FRCI detects FRLCyano at low abundance more sensitively than pigment analysis does. FRCI can also resolve the composition of FRLCyano at the genus level, which pigment analysis cannot do. In addition, we applied FRCI to eleven hot springs and five wetlands in Taiwan, showing that more diverse FRLCyano can be found in hot springs than in wetlands. Unexpectedly, Fischerella spp. were only found in four out of eleven hot springs in Taiwan, which is different from most hot springs in other places where Leptolyngbya and Fischerella dominate. We also isolated several previously unrecorded FRLCyano strains from hot springs in Taiwan, indicating that a combination of sequence-based and culture-based methods can effectively uncover the diversity of FRLCyano. Our study demonstrates that FRCI is a sensitive approach for detecting FRLCyano in the environment with great resolution.

Postfire resilience of soil bacterial communities in two Pinus species with contrasting fire adaptations

摘要：

Pine species interact with wildfire through two distinct adaptive strategies: fire-tolerance, as observed in Pinus taiwanensis (subgenus Pinus), and fire-avoidance, as seen in Pinus morrisonicola (subgenus Strobus). With the increasing frequency and intensity of forest fires driven by global climate change, understanding the responses of pines and their associated soil ecosystems is very important. In this study, we investigated the resilience of soil microbial communities in relation to these adaptive strategies by assessing soil properties and microbial communities one to three years postfire. Wildfire induced immediate changes in soil properties, including increased pH and decreased soil carbon, nitrogen, and electrical conductivity, with a gradual recovery over the following three years. Microbial diversity significantly increased postfire, with P. morrisonicola exhibiting higher diversity compared to P. taiwanensis. The P. morrisonicola site was characterized by fire-resistant bacterial taxa, whereas the P. taiwanensis site was dominated by opportunistic bacteria. Sensitive bacterial populations declined by 30% in P. morrisonicola and 48% in P. taiwanensis. The impact of the wildfire on soil microbes were more pronounced in P. taiwanensis., while changes in P. morrisonicola resembled those in unburned sites over the three- year period.

Unraveling Microbial Diversity and its Impact on Nitrification in a Full-scale Wastewater Treatment System

摘要：

Nitrification, the aerobic oxidation of ammonia to nitrate, is driven by phylogenetically conserved groups of microorganisms and serves as the rate-limiting step in determining nitrogen removal performance at wastewater treatment plants (WWTPs). While previous studies have primarily focused on the direct influence of nitrifying microorganisms on nitrification, the impact of broader microbial community properties, such as biodiversity and community dynamics, remains underexplored. This study investigates the relationship between microbial diversity and nitrification performance at a full-scale WWTP. We hypothesized that "noise" microbes, which do not directly contribute to nitrification, obscure the link between biodiversity and nitrification performance. To address this, we analyzed the total community and subset it into two categories: the nitrifier sub-community (taxa performing nitrification) and nitrifier-associated sub-communities (taxa directly or indirectly interacting with nitrifiers). Using multiple linear regression, we assessed alpha (number and abundance of taxa) and beta diversity (difference between communities) of the total community and the sub-communities for their relationship with nitrification rate. Our results showed that the diversity of nitrifier-associated sub-communities better explained the nitrification rate than the total community or nitrifier sub-community alone. Additionally, excluding nitrifier-associated taxa with weak association with nitrifiers improved the explanatory power of the sub-community diversity for nitrification. These findings highlight the critical role of microbial interactions in shaping nitrification performance in WWTP ecosystems and emphasize the influence of non-nitrifying microbes in shaping nitrification through their interactions with nitrifiers, offering new insights into optimizing microbial community management for improved nitrogen removal.