Trophic Modes Research Articles

Growth and Cell Size of Microalga Auxenochlorella protothecoides AS-1 under Different Trophic Modes.

Certain microalgal species can grow with different trophic strategies depending on the availability of nutrient resources. They can use the energy from light or an organic substrate, or both, and can therefore be called autotrophs, heterotrophs, or mixotrophs. We recently isolated a microalgal strain from the microplastic biofilm, which was identified as Auxenochlorella protothecoides, AS-1. Strain AS-1 grew rapidly in bacterial culture media and exhibited different growth rates and cell sizes under different trophic conditions. We compared the growth performance of AS-1 under the three different trophic modes. AS-1 reached a high biomass (>4 g/L) in 6 days under mixotrophic growth conditions with a few organic carbons as a substrate. In contrast, poor autotrophic growth was observed for AS-1. Different cell sizes, including daughter and mother cells, were observed under the different growth modes. We applied a Coulter Counter to measure the size distribution patterns of AS-1 under different trophic modes. We showed that the cell size distribution of AS-1 was affected by different growth modes. Compared to the auto-, hetero- and mixotrophic modes, AS-1 achieved higher biomass productivity by increasing cell number and cell size in the presence of organic substrate. The mechanisms and advantages of having more mother cells with organic substrates are still unclear and warrant further investigations. The work here provides the growth information of a newly isolated A. protothecoides AS-1 which will be beneficial to future downstream applications.

Metabolic responses of Euglena gracilis under photoheterotrophic and heterotrophic conditions

The protist Euglena gracilis has various trophic modes including heterotrophy and photoheterotrophy. To investigate how cultivation mode influences metabolic regulation, the chemical composition of cellular metabolites of Euglena gracilis grown under heterotrophic and photoheterotrophic conditions was monitored from the early exponential phase to the mid-stationary phase using two different techniques, i.e, nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HRMS). The combined metabolomics approach allowed an in-depth understanding of the mechanism of photoheterotrophic and heterotrophic growth for biomolecule production. Heterotrophic conditions promoted the production of polar amino and oxygenated compounds such as proteins and polyphenol compounds, especially at the end of the exponential phase while photoheterotrophic cells enhanced the production of organoheterocyclic compounds, carbohydrates, and alkaloids.

Succession of bacterial and fungal communities during the mud solarization of salt-making processing in a 1000-year-old marine solar saltern

A 1000-year-old marine solar saltern in Hainan Island, South China, is in the continuation of traditional skills involving mud soak and solarization for three days to accumulate salt, which is a unique process contributing to the selection of highly halophilic microbes related to salt quality and flavor. Herein, the successions of physicochemical properties and bacterial and fungal communities of muds from the saltern were investigated during the processing of mud solarization. The results showed that Na+, Cl−, Mg2+ and total nitrogen were the main factors in explaining the fluctuation of the fungal community, whereas the bacterial community was predominantly determined by Ca2+, total kalium and total phosphorus. During three days of mud solarization, the soil bacterial alpha diversity in the saltern was significantly lower than that of the surroundings, whereas the fungal alpha diversity showed an opposite trend. The bacterial functional groups with the same survival and adaptation strategies remained relatively stable, while the dominant functional type in fungi changed from monotropic to complex trophic mode. Additionally, some unidentified fungi species were increasingly found in mud. The abundances of Saitozyma, Solicoccozyma and Wallemia (Basidiomycota) increased and may contribute to the salt flavor through decomposing cellulose molecules into glucose due to their higher β-glucosidase activity, while the harmful fungal genera including Inocybe and Paraconiothyrium decreased obviously due to the stresses of salinity and solar exposure. These results showed that the traditional salt-making skills associated with mud solarization have selected a high abundance of beneficial halophilic microbes to increase the salt quality and flavor. Our findings not only reveal the underlying mechanisms for the long-history salt-making skills of this 1000-year-old unusual cultural heritage but also are highly valuable for bioprospecting to develop novel halophilic bacteria and fungi for modern chemistry industries.

Interactions between bacteria and microalgae in microalgal-bacterial symbiotic wastewater treatment systems: mechanisms and influencing factors

Microalgal-bacterial symbiotic wastewater treatment systems (MBSWTSs) have received widespread attention due to their capacity to achieve high pollutant removal efficiency during wastewater treatment, with low energy consumption requirements, efficient carbon sequestration, and wastewater resource utilization. This paper provides an overview of the treatment performance and current research status of MBSWTSs, including a detailed summary of the mechanisms of nitrogen, phosphorus, and carbon removal by MBSWTSs and the interactions between bacteria and microalgae. In particular, this review focuses on the influence of operational parameters on the regulation of the symbiotic system, such as the microalgal:bacterial ratio, N:P ratio, external carbon source, dissolved oxygen concentration, aeration mode, and light availability. Among these factors, the microalgal:bacterial ratio, carbon source, and light availability have an important influence on microalgal-bacterial competition, as well as the trophic mode of the system, biomass production, and the capacity for the process to be practically applied on a large scale. MBSWTSs still have some challenging aspects that have hindered their development and application, such as the unknown mechanism of microalgal-bacterial co-metabolism, limited previous practical applications, algal contamination, and harvesting difficulties. To overcome these challenges, future research requires a multidisciplinary approach, incorporating life sciences, material science, and other disciplines. Comprehensive research should be conducted on the metabolic mechanisms of MBSWTSs, the optimization of process performance and waste resource utilization, providing a theoretical and practical foundation for the practical application of MBSWTSs.

Profiling of fungal communities in functional food Cistanches herba using high–throughput sequencing

Cistanches Herba (CH), known as Roucongrong, is a widely used health food supplement and medicinal herb. In recent years, fungal and mycotoxin contamination has affected the quality and safety of CH, posing a potential threat to consumer health. In this study, the Illumina MiSeq PE300 platform and targeted the internal transcribed spacer 2 sequences were used to investigate fungal communities in CH. The differences in the fungal communities of samples from different collection areas and processing methods were analyzed. As a result, 606 ASVs were obtained and were further classified into six phyla, 27 classes, 56 orders, 110 families, and 167 genera. Basidiomycota and Rhizopodaceae were the dominant phylum and family, respectively. Rhizopus (0%–43.72%), Aspergillus (0%–19.55%), and Fusarium (0%–20.27%) were the most dominant genera among the identified genera. Meanwhile, 13 species were identified, including two potential toxigenic fungi Aspergillus terreus and and Mucor circinelloides. In addition, variations in the composition of the fungal communities, the diversity of fungi, their trophic modes, and the functional guilds in CH samples from four different collection regions and two processing methods were observed. This work provides useful information for controlling fungal contamination in herbs and foods to ensure food safety and human health.

Simultaneous production of algal biomass and lipid by heterotrophic cultivation of linoleic acid-rich oleaginous microalga Chlorella sorokiniana using high acetate dosage

The low-cost carbon source, acetate, was utilized to feed a linoleic acid-rich Chlorella sorokiniana for microalgal biomass and lipid accumulation. Remarkably high tolerance capability to high acetate dosage up to 30 g/L was observed, with heterotrophy being the preferred trophic mode for algal growth and lipogenesis when supplemented 20 g/L acetate. Transcriptome analysis revealed a marked activation of pathways involved in acetate bioconversion and lipogenesis upon exposure to high-level of acetate. However, the enhancement of photorespiration inhibited photosynthesis, which ultimately led to a decrease in biomass and lipid under mixotrophy. Heterotrophic acetate-feeding generated more superior amino acid profiling of algal biomass and a predominant linoleic acid content (50 %). Heterotrophic repeat fed-batch strategy in 5 L fermenter significantly increased the growth performance and lipid titer, with the highest levels achieved being 23.4 g/L and 7.0 g/L, respectively. This work provides a viable approach for bio-products production through acetate-based heterotrophic algal cultivation.

Amino acids rich biomass cultivation: Trophic mode influence on Chlorella Growth Factor (CGF) production

Nutritional supplement derived from protein-rich microalgae holds significant promise for both livestock and mankind. Chlorella sp. is unique and advantageous due to its ease of cultivation and presence of high composition of proteins, amino acids, and essential micronutrients. A comprehensive three-stage evaluation was conducted to assess different trophic modes (autotrophic, mixotrophic, and photoheterotrophic) and their impact on biomass production and nutritive value. These stages involved trophic mode cultivation (Stage-I) with varied carbon and nitrogen concentrations compared to nutrient deprived condition (control (N1)), CGF production and extraction (Stage-II), and CGF application (Stage-III). In Stage I, mixotrophic modes (M1 and M2) demonstrated the highest biomass production at 4.91 and 4.98 g L-1, surpassing autotrophic (A1 and A2), photoheterotrophic (H1), and nutrient-deprived (N1) conditions. Kinetic modelling revealed a correlative dependence of Chlorella sorokiniana growth on the supplemented nutrients. Scaling up the condition (M1) in a 5 L photobioreactor in Stage-II yielded a biomass of 4.63 g L-1 which was subjected to CGF extraction. In stage-II, C. sorokiniana exhibited a higher quantum efficiency of photosystem II (Fv/Fm: 0.77) and nutritive value, including 412.2 mg g-1 protein and 308 mg g-1 carbohydrate. Extracted CGF constituted of 54.4 % protein having eight essential amino acids (EAA) at 26.36 %, with a total EAA content of 13.7 g/100 g, slightly exceeding commercially available soy meal (12.5 g/100 g). In Stage-III, the applicability of CGF as a substrate for ethanol production using Saccharomyces cerevisiae was assessed, resulting in a biomass of 1.71 g L-1 and ethanol production of 4.5 %. This underscores the potential of C. sorokiniana not only as a rich nutritional source but also for the production of biobased products.

Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme’s activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle’s electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.

Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes.

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme's activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle's electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.

Soil fungal community is more sensitive than bacterial community to modified materials application in saline-alkali land of Hetao Plain.

Soil salinization has become a major challenge that severely threatens crop growth and influences the productivity of agriculture. It is urgent to develop effective management measures to improve saline-alkali soil. Thus, in this study, soil properties, microbial communities, and function under desulfurization gypsum (DE), soil amendment (SA), farm manure (FA), and co-application of desulfurization gypsum, soil amendment, and farm manure (TA) in a field experiment were examined by high-throughput sequencing. The results showed that the application of modified materials is an effective approach in improving saline-alkali soil, especially TA treatment significantly increased the content of available phosphorus (AP), available potassium (AK), soil organic matter (SOM), and alkaline hydrolysis nitrogen (AHN) and decreased pH, bulk density (BD), and electrical conductivity (EC). The application of modified materials resulted in notable enhancement in fungal diversity and altered the composition and structure of the fungal community. Conversely, the effect on the bacterial community was comparatively minor, with changes limited to the structure of the community. Regarding the fungal community composition, Ascomycota, Mortierellomycota, and Basidiomycota emerged as the dominant phyla across all treatments. At each taxonomic level, the community composition exhibited significant variations in response to different modified materials, resulting in divergent soil quality. The TA treatment led to a decrease in Mortierellomycota and an increase in Ascomycota, potentially enhancing the ability to decompose organic matter and facilitate soil nutrient cycling. Additionally, the sensitivity of fungal biomarkers to modified materials surpassed that of the bacterial community. The impact of modified materials on soil microbial communities primarily stemmed from alterations in soil EC, AP, AK, and SOM. FUNGuild analysis indicated that the saprotroph trophic mode group was the dominant component, and the application of modified materials notably increased the symbiotroph group. PICRUSt analysis revealed that metabolism was the most prevalent functional module observed at pathway level 1. Overall, the application of modified materials led to a decrease in soil EC and an increase in nutrient levels, resulting in more significant alterations in the soil fungal community, but it did not dramatically change the soil bacterial community. Our study provides new insights into the application of modified materials in increasing soil nutrients and altering soil microbial communities and functions and provides a better approach for improving saline-alkali soil of Hetao Plain.

Body fossil assemblages from the Lower Idzików Beds (Coniacian) in the Upper Nysa Kłodzka Graben, south-west Poland: Preliminary taphonomic, palaeoecological and palaeogeographical data

From mudstones and sandstones referred to as the Lower Idzików Beds, as exposed at Stary Waliszów (Upper Nysa Kłodzka Graben, south-west Poland), a rich assemblage of body fossils has been recovered. This comprises rare ammonites (Baculites incurvatus, Forresteria cf. petrocoriensis, ?Scalarites sp.), nautiloids (Anglonautilus sinuatoplicatus), numerous bivalves, inclusive of inoceramids such as Inoceramus frechi and Volviceramus involutus, oysters (Ceratostreon, Vultogryphaea and Hyotissa) and other common genera such as Scabrotrigonia, Protocardia, Cucullaea, Neithea, Pinna, Liopistha, Panopea and Goniomya. Gastropods include mainly aporrhaids, turritellids, naticids and ampullinids. Echinoids are rare and comparatively poorly preserved, comprising only irregular forms (cardiasterids, micrasterids and hemiasterids), some of them being recorded from the Upper Cretaceous of Poland for the first time. Decapod crustaceans are fairly abundant in the Lower Idzików Beds, with axiideans predominating. A taphonomic analysis shows that this assemblage is well preserved, suggesting rapid burial as a result of storm events, while a palaeoecological assessment of taxonomic composition and trophic modes implies that deposition took place in a shallow-marine, well-oxygenated environment with a soft-bottom substrate, rich in nutrients and close to the fair-weather wave base. The presence of stenohaline taxa such as ammonites and echinoderms provides evidence of normal salinity.

Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates.

As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.

Structure and assembly process of skin fungal communities among bat species in northern China.

The skin fungal communities of animals play a crucial role in maintaining host health and defending against pathogens. Because fungal infections can affect the skin microbiota of bats, gaining a comprehensive understanding of the characteristics of healthy bat skin fungal communities and the ecological processes driving them provides valuable insights into the interactions between pathogens and fungi. We used Kruskal-Wallis tests and Permutational Multivariate Analysis of Variance (PERMANOVA) to clarify differences in skin fungal community structure among bat species. A Generalized Linear Model (GLM) based on a quasi-Poisson distribution and partial distance-based redundancy analysis (db-RDA) was performed to assess the influence of variables on skin fungal communities. Using community construction models to explore the ecological processes driving fungal community changes, t-tests and Wilcoxon tests were used to compare the alpha diversity and species abundance differences between the fungal structure on bat species' skin and the environmental fungal pool. We found significant differences in the composition and diversity of skin fungal communities among bat species influenced by temperature, sampling site, and body mass index. Trophic modes and skin fungal community complexity also varied among bat species. Null model and neutral model analysis demonstrated that deterministic processes dominated the assembly of skin fungal communities, with homogeneous selection as the predominant process. Skin fungal communities on bat species were impacted by the environmental fungal reservoir, and actively selected certain amplicon sequence variants (ASVs) from the environmental reservoir to adhere to the skin. In this study, we revealed the structure and the ecological process driving the skin fungal community across bat species in northern China. Overall, these results broaden our knowledge of skin fungal communities among bat species, which may be beneficial to potential strategies for the protection of bats in China.

Responses to and detoxification of esculin in white-rot fungi

Plant metabolites have a great potential for limiting the spread of harmful fungi. However, a better understanding of the mode-of-action of these molecules and the defense systems developed by fungi to resist them, is needed to assess the benefits/risks of using them as antifungal treatment. White-rot fungi are excellent models in this respect, as they have adapted to the hostile habitat that is wood. In fact, wood is a source of putative antifungal compounds that can be derived using extraction techniques. In this study, we demonstrated that esculin and esculetin, which are coumarins found in plants and wood, reduce the growth of the wood-rotting fungi Fomitiporia mediterranea, Phanerochaete chrysosporium, Pycnoporus cinnabarinus and Trametes versicolor. We have shown that extracellular strategies are developed by the fungi to deal with esculin, through the involvement of laccases, peroxidases and glycoside hydrolases, and intracellular strategies, mainly via upregulated protein translation. Comparative proteomic and metabolomic approaches revealed that, despite the fact that the species analysed are closely related (they all belong to the Agaricomycetes, and have the same trophic mode), their defense responses to esculin differ.

Optimizing ciprofloxacin removal through regulations of trophic modes and FNA levels in a moving bed biofilm reactor performing sidestream partial nitritation

The performance of partial nitritation (PN)-moving bed biofilm reactor (MBBR) in removal of antibiotics in the sidestream wastewater has not been investigated so far. In this work, the removal of ciprofloxacin was assessed under varying free nitrous acid (FNA) levels and different trophic modes. For the first time, a positive correlation was observed between ciprofloxacin removal and FNA levels, either in the autotrophic PN-MBBR or in the mixotrophic PN-MBBR, mainly ascribed to the FNA-stimulating effect on heterotrophic bacteria (HB)-induced biodegradation. The maximum ciprofloxacin removal efficiency (∼98 %) and removal rate constant (0.021 L g−1 SS h−1) were obtained in the mixotrophic PN-MBBR at an average FNA level of 0.056 mg-N L−1, which were 5.8 and 51.2 times higher than the corresponding values in the autotrophic PN-MBBR at 0 mg FNA-N L−1. Increasing FNA from 0.006 to 0.056 mg-N L−1 would inhibit ammonia oxidizing bacteria (AOB)-induced cometabolism and metabolism from 10.2 % and 6.9 % to 6.2 % and 6.4 %, respectively, while HB-induced cometabolism and metabolism increased from 31.2 % and 22.7 % to 41.9 % and 34.5 %, respectively. HB-induced cometabolism became the predominant biodegradation pathway (75.9 %-85.8 %) in the mixotrophic mode. Less antimicrobial biotransformation products without the piperazine or fluorine were newly identified to propose potential degradation pathways, corresponding to microbial-induced metabolic types and FNA levels. This work shed light on enhancing antibiotic removal via regulating both FNA accumulation and organic carbon addition in the PN-MBBR process treating sidestream wastewater.

Variations in Chlorella lipid content in commercial and in-lab produced biomass

Microalgae appear as a sustainable source of biomass with relevant nutritional qualities. Still, regulatory restrictions currently limit the use of eukaryotic microalgae for human consumption to a short list of species dominated by Chlorella spp. Chlorella biomass contains valuable proteins but also interesting lipids, including polyunsaturated fatty acids (PUFA) ω3 and ω6. The amount of PUFA and the ω6/ω3 ratio vary significantly depending on the species and cultivation trophic mode. While the lipid profils of in-lab produced Chlorella has been widely studied, the variability of lipid content in commercial biomasses is barely described. Here, lipid classes and fatty acid profiles of six commercial biomasses of Chlorella spp. as well as those of lab-produced C. sorokiniana grown in photo-autotrophy and in four mixotrophy conditions were characterized. Results showed significant lipid composition variations between the biomasses, such as the triacylglycerols/glycolipids and ω6/ω3 contents. The ω6/ω3 ratios were lower in photo-autotrophic mode (2.5) while they ranged between 1.3 and 8.9 in commercial biomasses. The free fatty acids level was also variable (1.4% to 17.9% of total lipids). As a consequence, Chlorella lipid content and quality differed significantly, impacting the potential nutritional benefits of the consumption of commercial biomass. Processing and post-processing conditions should therefore be carefully controlled to optimize lipid profiles.

Fungal community structure shifts in litter degradation along forest succession induced by pine wilt disease

Fungi play a crucial role in decomposing litter and facilitating the energy flow between aboveground plants and underground soil in forest ecosystems. However, our understanding how the fungal community involved in litter decomposition responds during forest succession, particularly in disease-driven succession, is still limited. This study investigated the activity of degrading enzyme, fungal community, and predicted function in litter after one year of decomposition in different types of forests during a forest succession gradient from coniferous to deciduous forest, induced by pine wilt disease. The results showed that the weight loss of needles/leaves and twigs did not change along the succession process, but twigs degraded faster than needles/leaves in both pure pine forest and mixed forest. In pure pine forest, peak activities of enzymes involved in carbon degradation (β-cellobiosidase, β-glucosidase, β-D-glucuronidase, β-xylosidase), nitrogen degradation (N-acetyl-glucosamidase), and organic phosphorus degradation (phosphatase) were observed in needles, which subsequently declined. The fungal diversity and evenness (Shannon’s diversity and Shannon's evenness) dropped in twig from coniferous forest to mixed forest during the succession. The dominant phyla in needle/leaf and twig litters were Ascomycota (46.9%) and Basidiomycota (38.9%), with Lambertella pruni and Chalara hughesii identified as the most abundant indicator species. Gymnopus and Desmazierella showed positively correlations with most measured enzyme activities. Functionally, saprotrophs constituted the main trophic mode (47.65%), followed by Pathotroph-Saprotroph-Symbiotroph (30.95%) and Saprotroph-Symbiotroph (10.57%). The fungal community and predicted functional structures in both litter types shifted among different forest types along the succession. These findings indicate that the fungal community in litter decomposition responds differently to disease-induced succession, leading to significant shifts in both the fungal community structure and function.

Effects of stand density on the structure of soil microbial functional groups in Robinia pseudoacacia plantations in the hilly and gully region of the Loess Plateau, China

Elucidating the responses of soil microbial functional groups to changes in stand density is crucial for understanding the sustainability of forest development. In this study, we obtained soil samples from Robinia pseudoacacia plantations of three different stand densities (low, middle, and high densities of 750, 1125, and 1550 trees ha−1, respectively) in the hilly and gully region of the Loess Plateau, China. We sought to determine the effects of stand density on the structure of soil microbial functional groups. Stand density had no significant effects on species diversity indices of fungal trophic modes or bacterial functional groups involved in carbon (C) cycling and nitrogen (N) cycling. However, differences in stand density substantially altered the composition of fungal functional groups. In low-density plantations, saprophytic fungi were the main trophic mode, with a high relative abundance of ∼62 %, whereas the fungal communities associated with middle- and high-density plantations were dominated by other fungi with a combined trophic mode, which accounted for ∼43 % and ∼41 % of the fungal trophic modes, respectively. Furthermore, we detected increases in the relative abundance of plant pathogens, nitrifiers, and nitrous oxide-denitrifying bacteria with increasing stand density. Results of the Monte Carlo test showed that soil pH influenced the composition of soil fungal (but not bacterial) groups. These findings suggested that a high density of trees might inhibit the decomposition of recalcitrant organic material and stimulate nitrous oxide emission, consequently decreasing soil nutrient availability and stimulating soil N loss. Moreover, high-density stands might increase the potential risk for plant disease. Overall, the present study suggested that reducing stand density to coverage between 750 and 1125 trees ha−1 would increase soil nutrient availability and prevent N loss from the soil. To verify these suppositions, further research is needed to determine the links between microbial functional groups composition and soil biogeochemistry.

Protists in hypoxic waters of Jinhae Bay and Masan Bay, Korea, based on metabarcoding analyses: emphasizing surviving dinoflagellates

Hypoxia can indeed impact the survival of protists, which play a crucial role in marine ecosystems. To better understand the protistan community structure and species that can thrive in hypoxic waters, we collected samples from both the surface and bottom waters during the hypoxic period in Jinhae and Masan Bays and the non-hypoxic period in Jinhae Bay. Subsequently, we utilized metabarcoding techniques to identify the protistan species. During hypoxia, with dissolved oxygen concentrations of 0.8 mg L<sup>-1</sup> in Jinhae Bay and 1.8 mg L<sup>-1</sup> in Masan Bay within the bottom waters, the phylum Dinoflagellata exhibited the highest amplicon sequence variants richness among the identified protist phyla. Following the Dinoflagellata, Ochrophyta and Ciliophora also displayed notable presence. In hypoxic waters of Jinhae and Masan Bays, we identified a total of 36 dinoflagellate species that exhibited various trophic modes. These included one autotrophic species, 14 mixotrophic species, 9 phototrophic species with undetermined trophic modes (either autotrophic or mixotrophic), 2 kleptoplastidic species, and 10 heterotrophic species. Furthermore, the hypoxic bottom water exhibited a greater number of heterotrophic dinoflagellate species compared to the non-hypoxic surface water within the same water column or the non-hypoxic bottom water. Therefore, feeding by mixotrophic and heterotrophic dinoflagellates may be partially responsible for their dominance in terms of the number of species surviving in hypoxic waters. This study not only introduces the initial documentation of 26 dinoflagellate species surviving in hypoxic conditions but also establishes a foundation for a more comprehensive understanding of the ecophysiology of dinoflagellates in hypoxic marine environments.

Interactions of long-term grazing and woody encroachment can shift soil biogeochemistry and microbiomes in savanna ecosystems

Semi-arid grasslands and savannas in the southern Great Plains USA are extensively used for livestock grazing. Over the past century, Juniperus (juniper) and Quercus (oak) species abundance have increased due to intensive grazing and reduced fire frequency. We investigated the interactions between livestock grazing history (none, moderate, heavy) and vegetation cover (grassland, juniper, oak) using a ∼ 70-year grazing experiment in west-central Texas. We explored effects on soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), microbial community composition, and function. SOC and TN were 50–150 % higher under juniper and oak compared to grasslands, and 10–30 % lower in grazed vs. ungrazed areas. Vegetation × grazing interaction showed greater SOC and TN loss under oak than juniper or grasslands. Ungrazed controls had higher soil TP than grazed areas, with oak and juniper soils having more TP than grasslands. Bacterial and fungal communities differed between grassland and woody vegetation. Grazing affected only bacterial communities. SOC, TN, TP accounted for differences in community structure. Abundances of genes related to methane, nitrogen, sulfur metabolisms, and dominant fungal trophic modes were linked to soil C, N, P ratios. These findings highlight how long-term livestock grazing and woody plant encroachment influence soil C, N, P cycles, altering soil microbial community structure and function. This study provides insights for savanna ecosystem management and integrating land cover effects into biogeochemical models for global change scenarios.