分類學 (Taxonomy) 是人類描述並理解生物多樣性的基礎，其中既以科學 (Science) 為骨幹，卻也包含人為判斷的藝術 (Art)。藉由建立一組階層式的分群 (Classification) 架構和一套被廣泛接受的命名 (Nomenclature) 系統，分類學提供了溝通的關鍵工具，不論是科學研究，亦或是教育、法規等面向皆相當重要。近年來由於演化基因體學的快速發展，相關的思維及工具逐漸被應用在細菌分類學之中。藉由本實驗室在農桿菌 (Agrobacteria) 及柔膜菌綱 (Mollicutes) 等分類群的研究為例，本演講將探討如何結合分子演化與基因體序列分析，思考在「種」 (Species) 和「屬」 (Genus) 層級的細菌分類議題。

氣候變遷的成因眾多，最主要的原因就是溫室氣體的大量排放。為了避免全球暖化失控，聯合國多次召開氣候峰會，簽訂各項氣候協定，致力於降低二氧化碳與甲烷等溫室氣體的排放，並宣示在2050年達到「淨零排放」的目標。甲烷所造成的暖化效應是同量二氧化碳的25 倍。截至去年12月底，全球共155個國家簽署「全球甲烷承諾」，宣示在2030年前要減少30% 以2020 年為基準的甲烷排放量，以減緩氣候危機。甲烷菌是地球上唯一能產生甲烷的微生物，隸屬於古菌域，是一種對氧氣極其敏感的絕對厭氧微生物。因為產甲烷的特性，甲烷菌「曾經」被視為生質能源或替代能源的明日之星。隨著「全球甲烷承諾」的簽訂，全世界滅甲烷的浪潮興起，甲烷菌一夕成為萬惡的淵藪，各式甲烷減排研究風生水起，甚至已有牛隻減排飼料上市。然而，隨著科學家開始體認「甲烷清零」的不可行性，近年各國政府又開始重視並投入沼氣發電。國內花蓮璞石閣畜牧生質能源中心與永豐餘公司等，在沼氣發電都有相當好的進展。做好甲烷收集系統，嚴密控制洩漏逸散，完整用於發電，做好發電後二氧化碳收集捕捉再利用系統；甲烷菌將能扮演廢物變能源及能源無限循環再生的關鍵角色。

The epiphytic bird's nest ferns (Asplenium nidus) in the forest canopy resemble distinctive island habitats for microbes due to their abundant suspended leaf litter and soil. Although research has shown that plants can actively structure the surrounding microbiome by root exudates and species-specific litter chemistry, it is unclear whether A. nidus plays a similar role. This study aims to understand whether A. nidus acts as passive islands or active drivers of microbiomes in their suspended soil. We examined 24 A. nidus individuals of varying sizes (small, medium, and large) in a Cryptomeria japonica plantation in Wulai, Taiwan. Soil samples were collected from small individuals and different layers in medium and large individuals. The Fungal community was characterized using the rDNA ITS1 region. In line with the theory of island biogeography, we showed that the fungal OTU richness significantly increased with the size of A. nidus. Moreover, the pH range (i.e., differences in pH value between the top and bottom of A. nidus individuals) increased with the size of A. nidus and is positively correlation with the mean dissimilarity between fungal community composition within the A. nidus individual. However, we found no convergence of fungal community composition with the size of A. nidus, which may imply that A. nidus will not actively structure the fungal community through time. Overall, our results suggest that A. nidus function as islands, with their growth providing diverse niches that foster fungal diversity.

Ammonia is a well-known aquatic nitrogenous pollutant that threatens fish health, particularly in aquaculture. The fish skin with mucus and residing microbiome serve as the primary external interface between the fish host and aquatic environment. However, how this fish skin interface responds to ammonia remains unexplored. The present study thereby conducted an ammonia challenge on striped catfish with or without removing skin mucus. Both skin responses and the associated skin mucus microbiome were examined. We found that ammonia could damage fish skin tissue by inducing epidermal exfoliation and inflammation, yet the skin mucus could reduce this damage. We also observed changes in associated microbiome composition and metabolic function by 16S rRNA gene sequence and Ecoplate assay. Cultivation of the skin mucus in an ammonia-enriched medium showed significant ammonia reduction, suggesting potential ammonia-utilizing bacteria in the skin mucus microbiome. Further isolation identified Acinetobacter sp. as one of the ammonia-utilizing bacteria in the skin mucus microbiome. These data suggest that the potential ammonia-utilizing bacteria in the skin microbiome may mitigate ammonia for buffering skin tissue damage. This study sheds some light on the complex interplay between environmental ammonia and host skin under the intervention of the skin microbiome. Understanding how fish skin and its mucus microbiome respond to ammonia-enriched environments will help develop a better aquaculture practice monitoring fish health.

The Taoyuan Algal Reef, one of the world’s largest algal reef ecosystems formed by crustose coralline algae (CCA), faces severe pressure from industrial development and pollution. While the responsiveness of the microbial community makes it a great indicator for evaluating habitat pollution or host health conditions, the microbial composition of the Taoyuan Algal Reef remains unexplored. To further understand the microbiome in the Taoyuan Algal Reef and site variations, we collected two dominant algae species from Datan, Yongxing, and Baiyu. Our results reveal significant differences in microbial composition between the three sampling sites, with Datan and Yongxing exhibiting greater similarity. Furthermore, biomarkers identified in Datan, Yongxing, and Baiyu are found to be closely associated with microbial strains from coral reefs, algae, or extreme habitats, respectively. These results suggest there may be environmental disparities between the sampling sites. Indeed, the predicted microbial functional genes associated with heavy metals and the nitrogen cycle are clustered according to the sampling sites, further implying potential pollution-induced differences. Our study provides an example of applying microbiome analysis to evaluate habitat conditions, offering clues and narrowing down factors contributing to the differences between habitats. Further investigation is crucial to validate the predicted results.

White-tailed deer (Odocoileus virginianus) is one of the most widely distributed wildlife species in the United States and deer farming is a growing industry in Florida. Viral hemorrhagic diseases and bacterial infections have been identified as significant contributors to mortality in farmed white-tailed deer in Florida, resulting in substantial production loss and potential threats to wildlife. Nevertheless, a knowledge gap remains regarding other emerging viral pathogens in Florida's white-tailed deer population that could similarly impact production. This study aims to elucidate the special heterogeneity, possible origins, and transmission routes for bovine viral diarrhea virus (BVDV) and mule deerpox virus (MDPV), both identified as emerging viral pathogens in the Florida white-tailed deer. The University of Florida Cervidae Health Research Initiative (CHeRI) provides diagnostic services to Florida deer farmers for the determination of cause of death and disease surveillance. From 2016 to date, participating Florida ranches provided recently deceased farmed white-tailed deer or shipped samples for necropsy and analysis through the CHeRI diagnostic program. We identified four cases of BVDV2 with severe hemorrhage on two farms in Florida white-tailed deer in 2018. Furthermore, in 2022, three cases of stillborn white-tailed deer carrying BVDV1 on a separate farm were identified. The genome sequence data showed that BVDV2 from our cases is highly similar to the BVDV2a found in beef cattle in other states in the US, suggesting the possibility of cross-species transmission. This is the first report of BVDV in white-tailed deer in Florida; with this finding, disease surveillance is crucial at the wildlife-livestock interface to prevent potential outbreaks among host species. Since 2017, a comprehensive necropsy analysis of 148 cases exhibiting skin lesions has yielded significant findings, with 50 cases testing positive for MDPV. MDPV cases exhibit a statewide distribution in Florida, particularly impacting animals aged 2 to 12 weeks, with the highest case numbers occurring during the summer months. Our results show that MDPV can be detected through conventional PCR from not only skin and tongue lesion tissue and lesion swabs, but also from most internal organ tissue collected during necropsy, such as lung, heart, and spleen. Genome data has shown that the MDPV in this study is identical to the first detected MDPV in Florida in 2016, suggesting that MDPV is very conservative over time within the farmed deer population. Future works aim to understand viral ecology by identifying possible vectors and incorporating animal transmission data. Our results will provide valuable information to improve preventative health measures and clinical management of both wild and captive white-tailed deer in Florida, especially at the wildlife-livestock interface.

含氮物質污染為21世紀最具挑戰的環境問題之一。人們日常生活產生的都市污水為水量最大的污染，含有20-60 mg-N/L的氮，為主要的氮污染來源。部分硝化-厭氧銨氧化(Partial Nitritation-Anammox, PN-A)為一永續生物除氮程序，由好氧的氨氧化菌將氨氧化至亞硝酸，再由厭氧銨氧化菌在缺氧條件下將亞硝酸與氨轉換至氮氣。目前PN-A已可用於處理高濃度銨氮廢水，但處理低濃度廢水(<100 mg-N/L)仍相當困難。為使好氧的氨氧化菌與厭氧的厭氧銨氧化菌在同一反應槽中共存並和合作，並避免氨完全硝化至硝酸，通常需要控制在低溶氧-缺氧動態環境。然而在低溶氧與低氨氮濃度條件下，許多研究發現氨氧化菌活性不足，無法有效將氨氧化至亞硝成為PN-A處理低濃度廢水主要的瓶頸。2015年發現的完全氨氧化菌打破過去百餘年來對硝化作用的認知，能夠單獨將氨氧化至硝酸。近年來對完全氨氧化菌的研究發現其廣泛分布於各類廢水處理系統中，並在低溶氧與低銨濃度環境為優勢硝化菌群。我們認為完全氨氧化菌有潛力應用於PN-A程序處理低濃度廢水，解決氨氧化活性不足的問題。然而完全氨氧化菌進行部分硝化(NH3→NO2-)或是完全硝化(NH3→NO2-→NO3-)調控機制仍不清楚，這會導致與厭氧氨氧化菌不同的交互作用而影響PN-A程序的除氮效能。本研究透過一系列實驗探討(1)如何讓完全氨氧化菌與厭氧銨氧化菌共同優勢化，(2)如何控制完全氨氧化菌進行部分硝化，以及(3)PN-A系統中微生物體如何適應低溶氧-缺氧變動環境。我們的結果展示完全氨氧化菌其氨氧化與亞硝氧化的路徑可分開調控，在特定條件下進行部分硝化達成與厭氧銨氧化菌合作，此合作關係提供的生態服務能高效處理低濃度銨氮污水，成為淨零趨勢下重要的低碳廢水處理方法。

Microbial ecology and experimental microbiology are crucial to microbiology. Experimental microbiology isolates, cultivates, and characterizes microbial strains in controlled lab environments, while microbial ecology studies the microbial communities and the microbe-environment interactions. They may seem unconnected, but together, they can help solve problems. Cyanobacteria research illustrates the use of ecological and experimental methods to answer questions, such as how to better identify far-red light-utilizing cyanobacteria (FRLCyano) in the environment. Although most cyanobacteria use visible light (VL; λ= 400-700 nm) for photosynthesis, some have evolved strategies to acclimate to and use far-red light (FRL; λ= 700-800 nm). Numerous studies examine pigments, such as chlorophylls d and f, to investigate the presence of FRLCyano in the environment. This method is not ideal because it can only detect FRLCyano that have acclimated to make chlorophylls d or f. 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 produce microbial communities with a series of cyanobacteria and FRLCyano abundance levels. We found that FRCI detects FRLCyano more sensitive than pigment analysis. FRCI can also resolve the composition of FRLCyano at the genus level, which pigment analysis cannot do. In addition, we applied FRCI to published datasets and discovered putative FRLCyano in diverse environments, including soils, hot springs, and deserts. One new finding from this study is that, even after multiple subcultures, cyanobacterial growth conditions cannot reduce the relative abundance of some bacterial phyla (Planctomytota, Proteobacteria, and Bacterioidota) in the culture. Strangely, the cyanobacterial medium has been utilized for decades, but no one has studied microbiota change during enrichment. Lowering the relative number of other bacteria can improve cyanobacteria enrichment and axenic strain isolation. Thus, we selected several treatments for environmental samples and found that particular antibiotics can significantly increase the relative abundance of cyanobacteria in the microbial community. Our results demonstrate that ecological approaches can be combined with experimental approaches in solving questions.

The discovery of eukaryotic giant viruses, with genome and virion sizes similar to those of some bacteria, challenged the traditional view that viruses are small infectious entities. Recent advances in microbial genomic technologies, as well as numerous efforts to isolate, culture, and characterize environmental giant viruses, have led to the establishment of new giant virus families and identification of new eukaryotic hosts. Now we know that their hosts encompass all major lineages of eukaryotes, including many unicellular eukaryotes such as microalgae, amoebae, and other heterotrophic microeukaryotes. In addition to smallpox and African swine fever, giant viruses are lethal pathogens of many vertebrates and invertebrates, can cause rapid population crash in algal blooms and other protists, and are increasingly recognized for their role in facilitating the cycling of carbon stored in eukaryotic cells. In this talk, I will summarize our recent works using phylogenomic analyses of core proteins widely present in giant viruses to infer their evolutionary relationships and to reconstruct a time-calibrated phylogeny. To better understand virus-host interactions through time, we also focused on proteins that form an entry-fusion complex (EFC) to mediate virus entry in poxviruses. Two EFC gene families are widely distributed across other major lineages of Nucleocytoviricota and found in most giant viruses infecting animals or amoebozoans, but are generally absent in those infecting algae or non-amoebozoan heterotrophic protists. Distribution and phylogenetic patterns suggest that both families originated in the ancestor of Nucleocytoviricota, which implies the existence of a conserved membrane fusion mechanism and sheds light on host range and ancient evolution of giant viruses.

細菌在一般人的印象中，大致就是游來游去的單細胞生物，但他們平常生活在各種險峻的環境裡，往往能長成多細胞、結構嚴謹的生物膜。在很多面向上，生物膜很像多細胞生物。我們最近發現，枯草桿菌的生物膜和脊椎動物一樣，有體節生成的發育機制。生物膜會把自己的缺氮逆境反應在空間上分節成一圈一圈的同心圓紋路。而這個斑紋生成現象背後的分子機制，似乎是由個別細菌自主的分子時鐘驅動的。為了證實這個機制，我們用數學模擬找出調整分子時鐘週期的方法，並據此在實驗上成功增加了生物膜同心圓的圈數。我們更發現，生物膜會依據缺氮逆境反應的時空動態，決定細胞分化要在哪些位置發生，因而將分化的孢子也排列成同心圓的斑紋。細菌生物膜這個分節鐘的機制，雖在分子機制與生物目的上大相徑庭，在概念上卻和脊椎動物胚胎的體節發育極其相似。

To most people, bacterial cells are free-living single-cell organisms. However, in the real world, most bacteria can form structured, multicellular communities called biofilms. In many ways, biofilms resemble multicellular organisms like you and me. We recently discovered that Bacillus subtilis biofilms can develop into segments just like vertebrates. These biofilms can spatially pattern their nitrogen stress response into concentric rings. The molecular mechanism underlying this phenomenon seemed to be a cell-autonomous molecular clock within each bacterial cell. To support this hypothesis, we used mathematical modeling to figure out a way to tweak the period of the molecular clock. Accordingly, we successfully changed the number of concentric rings experimentally. We further demonstrated that sporulation, a cell differentiation event in the biofilm, is patterned according to the spatial-temporal dynamics of the nitrogen stress response, which also formed concentric rings. Although achieved using a completely different molecular circuit and for an entirely different biological purpose, the principle of segmentation is strikingly analogous to the segmentation clock used in vertebrate somitogenesis.

Carnivorous plant leaves, such as those of the spoon-leaved sundew Drosera spatulata, secrete mucilage which hosts microorganisms potentially aiding in prey digestion. We characterised the mucilage microbial communities and identified the acidophilic fungus Acrodontium crateriforme as the ecologically dominant species. The fungus grows and sporulates on sundew glands as its preferred acidic environment. We show that the A. crateriforme has a reduced genome similar to that of other symbiotic fungi. Based on the transcriptomes when encountering prey insects, we revealed a high degree of genes co-option in each species during fungus-plant coexistence and digestion. Expression patterns of the holobiont during digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating the digestion of sundew’s prey, as well as transporters and dose-dependent responses in plant genes involved in jasmonate signalling pathway. This study establishes that botanical carnivory is defined by multidimensional adaptations correlated with interspecies interactions.

Anaerobic degradation processes represent a pivotal biotechnological advancement, offering a sustainable solution for converting organic waste into renewable energy - a crucial stride towards an energy-neutral future. This anaerobic process involves a consortium of diverse microbes catalyzing the breakdown of organic compounds and metabolites into valuable biogas products, primarily methane. Although anaerobes can acquire the energy stored in organic waste for their growth, their metabolic process is inherently constrained by the thermodynamic bioenergetics of anaerobic degradation. To overcome the inherent thermodynamic limitations caused by the accumulation of metabolites like volatile fatty acids and H2, anaerobes must engage in tightly-knit interactions that profoundly influence the energy distribution released during organic degradation to benefit their growth and methane production. The interplay between metabolite profiles (or energy allocation) and microbial interactions in a reactor system forms a complex feedback loop that significantly shapes the community assembly and bioreactor performance over time. Despite its profound implications, understanding the dynamic nature of this interplay remains an unsolved puzzle, primarily due to the challenges in quantitatively characterizing microbial networks and their time-varying dynamic behaviors in highly fluctuating anaerobic reactors. This study employed a Multiview Distance Regularized (MDR) S-map approach to reconstruct high-dimensional time-varying interaction networks using 110 daily datasets from an anaerobic bioreactor converting sucrose to biogas post-start-up. The convergent cross-mapping method was then used to determine the causal relationship between the interaction network, metabolites, and community structure, elucidating the causation between time-series variables. In this presentation, I will share new insights after deciphering the dynamic interplay of sucrose-to-methane bioenergetics and network properties. This knowledge contributes to a better understanding of microbial energetics and networking, shedding light on microbial succession within the bioreactor and its impact on converting organic matter to biogas. This understanding is pivotal for optimizing bioreactor performance and advancing sustainable practices in the generation of renewable energy.

Microbialites are organosedimentary deposits formed through the interaction of complex microbial activities by diverse communities with their surrounding environment. They provide insight into the formation of the most ancient microfossil stromatolites with distinct laminations. To decipher the embedded information, researchers utilize modern microbialite as an analog to explore the interplay of microbes and environment. Our comparative study has unveiled contrasting differences in the microbial communities, potential activities, and formation environments for modern stromatolites (laminated microbialites) and thrombolites (clotted microbialites) in Kenting. Taxonomic analyses indicate that stromatolites have a dominant yet less diverse composition of cyanobacteria (23%). Moreover, stromatolites exhibit more mature microbial communities with a higher abundance of Archaea (4%) and Firmicutes (4%) compared to thrombolites (0.05% and 0.3%, respectively). In contrast, non-layered thrombolites exhibit a higher abundance (42%) and a more complex composition of cyanobacteria. The stratified and mature microbial communities in stromatolites exhibit a more balanced metabolic function and greater adaptation within their laminated microenvironment. FAPROTAX analyses reveal that stromatolites exhibit a higher metabolic potential for nitrite, nitrate, methanogenesis, and sulfur-related respiration compared to thrombolites, which, in turn, show a higher metabolic potential for ureolysis, photosynthesis, and phototrophic pathways. These findings not only unveil differences in microbial community composition but also shed light on dynamic metabolic potentials and coordinated microecological functions during the formation of modern microbialites.

腸道菌叢與宿主的交互作用，可直接或間接地影響宿主的免疫、代謝與神經傳遞功能，人體微生物叢的相關研究，讓過去許多不明病因的人類慢性與退化性疾病，開啟了一條全新的解方尋求之路。人類腸道微菌研究發展至今，已無法滿足於菌相與疾病相關性的發現，需將目標菌種分離培養出來，才可針對特定菌種進行更明確的機制探討。以心血管疾病為例，許多證據顯示腸道菌與飲食交互作用產生的活性分子，在心血管健康亦扮演重要角色。氧化三甲胺 (trimethylamine N-oxide, TMAO) 已被證實為導致心血管疾病的腸道菌代謝物，通常是腸道中的細菌代謝飲食中的肉鹼與膽鹼所生成。由於每個人腸道菌叢的不同，並非所有食用肉鹼的人都會產生 TMAO，造成了個人體質的差異。透過總體基因體 (metagenome) 分析結合厭氧菌培養體學 (anaerobic culturomics)，找到參與代謝肉鹼並生成 TMA/TMAO 的關鍵基因簇 bbuABCEDF，並將腸道中少數帶有 bbu 基因簇的菌種盡可能發掘出來，進行 γ-butyrobetaine (腸道菌代謝肉鹼產生TMA的中間產物) 代謝功能確認，發現帶有 bbu 基因簇的腸道菌與 TMAO 產能具顯著相關性，並將這些具功能性的 bbu 基因簇視為代謝肉鹼產生 TMA 的生物標記。我們已使用厭氧培養技術和特定菌定植小鼠建立腸道菌代謝 γ-butyrobetaine 生成 TMA/TMAO 活性測試平台，將腸道菌叢帶有 bbu 基因簇的腸道菌種分離培養出來，建立代謝 γ-butyrobetaine 生成 TMA 的菌種資源庫與基因資料庫，並設計特殊引子開發即時聚合酶連鎖反應 (qPCR) 檢測方法，以辨別攝取紅肉後體內腸道菌會產生大量 TMA 與 TMAO 的人類個體，作為個人化營養與精準健康的臨床轉譯工具。

The vast majority of prokaryotic species on Earth remain uncultured and uncharacterized, constituting a category of phylogenetically unaffiliated microbes that have been referred to as “microbial dark matter”. To gain insights into this mysterious microbial world, microbiologists rely extensively on culture-independent approaches such as meta- and single-cell omics. In order to identify specific microorganisms based on an in situ metabolism without hampering by insufficient sensitivity and habitat complexity, this study presents a novel approach to identify single microbial cells metabolizing a specific organic compound with high sensitivity and without prior knowledge of the microbial community. This workflow consists of several key steps, beginning with the labelling of individual cells within a community using a 14C substrate based on their metabolic activity. Subsequently, cells are encapsulated in photoemulsion-hydrogels through a microfluidics system. The application of microautoradiography (MAR) facilitates the visual differentiation between encapsulated labelled and non-labelled cells. Following this, flow-cytometric sorting of encapsulated cells is performed, and single-cell genomics is carried out on the labelled and sorted cells. Demonstrated through a proof-of-concept, this approach successfully separated and sequenced individual cells of the benzene degrader Pseudomonas veronii from mock microbial communities. This innovative method, named scMAR-Seq (Single Cell capturing via MicroAutoRadiography and microfluidics for genome Sequencing), holds promise for unravelling microbial identity and function across diverse habitats, making it a valuable tool for exploring novel taxa and genes with potential applications in biotechnological fields like bioremediation.

Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within one year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.

The gastrointestinal tract harbors a complex gut microbiota, which can be conceptualized as a supra-organism due to its enhanced functions surpassing those of individual organisms. This microbial consortium consists of a variety of bacterial taxa and a redundancy of functional genes, contributing to the stability of community functions even during abrupt ecological shifts. Despite this, the mechanisms by which a minimal microbial assemblage sustains specific metabolic functions remain poorly understood. In this study, we utilized a nine-species microbial community derived from rat cecum to explore the molecular and ecological interactions within a minimal microbial consortium. We identified two distinct sub-communities: an E. coli-dominated consortium and a cellulolytic consortium, differentiated through cultivation in a cellulose medium. The E. coli consortium exhibited a gene profile oriented towards amino acid metabolism and glycosidic bond formation, whereas the cellulolytic consortium possessed genes facilitating glycosidic bond degradation, potentially providing carbohydrate sources to the E. coli consortium. A simulation using the competitive Lotka-Volterra model indicated that this minimal community could achieve equilibrium, featuring co-existing sulfite-reducing E. coli and cellulose-dependent species. Our metagenomic analyses and studies of community dynamics demonstrate that such minimal communities exhibit functional and ecological complementarity. These findings align with the Black Queen Hypothesis and offer insights into the inseparability of certain bacteria from their complex symbiotic communities. 

We use the QUEEN-2m biosensor to quantify ATP dynamics in single Escherichia coli cells in relation to their growth rate, metabolism, cell cycle, and cell lineage. We find that ATP dynamics are more complex than expected from population studies and are associated with growth rate variability. Under a nutrient-rich condition, cells can display large fluctuations in ATP level that are partially coordinated with the cell cycle. Abrogation of aerobic acetate fermentation (overflow metabolism) through genetic deletion considerably reduces both the amplitude of ATP level fluctuations and the cell cycle trend. This suggests that overflow metabolism exhibits temporal dynamics, which contributes to fluctuating ATP levels during growth. Remarkably, at the single-cell level, growth rate negatively correlates with the amplitude of ATP fluctuation for each tested condition, linking ATP dynamics to growth rate heterogeneity in clonal populations.

Global fire regimes are shaped by vegetation types and tree species complexity. In the genus Pinus, two subgenera, Pinus and Strobus, exhibit distinct fire adaptation strategies. Pinus, adapted to fire-prone regions, features highly flammable, long needles and thicker bark, while Strobus, adapted to fire avoidance, has shorter leaves. The accumulation of slow-decomposing fallen on the forest floor elevates wildfire risks. However, the mechanisms linking plant traits and decomposing microbiomes, contributing to fire regime dynamics, remain unclear. In our six-month litterbag experiment in Taiwan, we studied P. taiwanensis (subgenus Pinus) and P. morrisonicola (subgenus Strobus). Litter chemical dynamics and microbial succession were assessed through 13C NMR and shotgun metagenomic sequencing, respectively. P. morrisonicola litter decomposed faster, influenced more by litter species than sites. Litter chemistry varied according with litter types and incubation sites. Fungal diversity at the species level increased during decomposition but decreased at the class level, positively correlated with decomposition rates. Fungi enriched in P. morrisonicola litter harbored abundant gene copies of lignocellulolytic enzymes. Gene abundances of cellulolytic enzymes were higher in the early decomposition, while those of ligninolytic enzymes were lower, reflecting substrate utilization. Our results suggested distinct fungal communities in the two forests, shaped by litter properties, leading to distinguishable decomposition rates between fire-avoiding and fire-tolerating pine species.