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Understanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon ( rrn ) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.

Plankton microorganisms play central roles in the marine food web and global biogeochemical cycles, while their distribution and abundance are affected by environmental variables. The determinants of microbial community composition and diversity in estuaries and surrounding waters with multiple environmental gradients at a fine scale remain largely unclear. Here, we investigated bacterial and protistan community assembly in surface waters from 27 stations across the Changjiang Estuary to the ocean, with salinity ranging from 0 to 32.1, using 16S rRNA and 18S rRNA gene amplicon sequencing. Statistical analyses revealed that salinity is the major factor structuring both bacterial and protistan communities. Salinity also acted as a significant environmental determinant influencing alpha-diversity patterns. Alpha diversity indices for bacterial and protistan communities revealed a species minimum in higher-salinity waters (22.1–32.1). Contrary to the protistan community, the highest bacterial diversity was identified in medium-salinity waters (2.8–18.8), contrasting Remane’s Artenminimum concept. The distribution of major planktonic taxa followed the expected pattern, and the salinity boundary for Syndiniales was specifically identified. These findings revealed the significant effects of salinity on the microbial community across an estuary to ocean transect and the distinct response to salinity between bacterial and protistan communities.

Background Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes. Results Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer. Conclusions We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers. 9YGnSNgqaHj2gH_1N6en5w Video abstract

Background Reductive soil disinfestation (RSD) is an effective agricultural practice to improve the soil microbial community. However, most RSD research has focused on single bacteria or fungi, little is known about the combined influence on the entire microbiome, particularly impacts on protists and the relationships of these groups linked to plant biomass in rhizosphere soil. Methods In this study, four treatments, i.e., untreated control (CK), RSD with 1% corn straw (CS), 1% miscanthus (MS), and 1% arundo donax (Ad) were performed. Results RSD treatment decreased bacterial and fungal community diversity, but increased the diversity of protistan community, along with the relative abundances of Cercozoa and Amoebozoa belonging to phagotrophic protists. The bacterial community diversity rapidly increased with plant growth in the RSD treatment, and we observed that the bacterial community diversity and structure were the major predictors of plant biomass. The RSD treatment had significantly lower relative abundances of potential pathogenic fungi (e.g., Fusarium and Cladosporium) compared to the CK treatment, and the CK treatment showed a dramatic decrease in fungal community diversity. Additionally, RSD treatment increased both bacteria-bacteria and bacteria-protist connections, as reflected by co-occurrence network analysis. The Mantel test demonstrated that soil pH and NO 3 − -N contents were intensively correlated with bacterial and protistan community diversity, respectively. Moreover, the Ad treatment had notably higher soil LOC and NO 3 − -N contents compared to the CK treatment after 90 days of plant growth. Conclusion RSD treatment promoted plant biomass by increasing soil nutrient turnover and inhibiting pathogen persistence through affecting more connections among soil microbial communities within the rhizosphere.

Integrated aquaculture, centered around polyculture involving multiple species, is a typical practice for the sustainable development of the aquaculture industry, capable of enhancing resource utilization efficiency, environmental stability, and overall productivity through establishing symbiotic interactions among species. This study employed multi-amplicon high-throughput sequencing to assess the ecological impacts of two polyculture methods involving river crabs on sediment bacteria, fungi, and protists. One method involved polyculturing river crabs with mandarin fish, silver carp, and the stone moroko (SPC), and the other involved polyculturing river crabs with only mandarin fish and silver carp (SMC). The results showed that, compared to the SMC group, the SPC group remarkably increased the Chao1 index of bacterial communities in pond sediment and decreased the Pielou_J index of protists. The relative abundances of all fungal phyla and most dominant bacterial and protistan phyla (top 10 in relative abundance) in the SPC group were considerably different from those in the SMC group. In the co-occurrence networks of bacterial, fungal, and protistan communities, the numbers of edges and nodes were higher in the SPC group than in the SMC group, and the habitat niche breadth of bacterial community was also notably increased in the SPC group. The levels of total carbon (TC), total nitrogen (TN), and phosphates within pond sediment in the SPC group were obviously lower than those in the SMC group, and were significantly correlated with the microbial communities, with TC being identified as the primary contributor driving changes in the microbial communities. All the findings collectively demonstrate that the polyculture of river crabs with mandarin fish, silver carp, and the stone moroko enhances the stability of bacterial, fungal, and protistan communities in sediment and enhances resource utilization efficiency in aquaculture, thereby preventing the environmental risks associated with excessive nutrient accumulation in sediment. Polyculture systems integrating river crabs with mandarin fish, silver carp, and the stone moroko represent a sustainable aquaculture model with significant ecological benefits.

Current global change is associated with an increase in disturbance frequency and intensity, with the potential to trigger population collapses and to cause permanent transitions to new ecosystem states. However, our understanding of ecosystem responses to disturbances is still incomplete. Specifically, there is a mismatch between the diversity of disturbance regimes experienced by ecosystems and the one-dimensional description of disturbances used in most studies on ecological stability. To fill this gap, we conducted a full factorial experiment on microbial communities, where we varied the frequency and intensity of disturbances affecting species mortality, resulting in 20 different disturbance regimes. We explored the direct and long-term effects of these disturbance regimes on community biomass. While most communities were able to recover biomass and composition states similar to undisturbed controls after a halt of the disturbances, we identified some disturbance thresholds that had long-lasting legacies on communities. Using a model based on logistic growth, we identified qualitatively the sets of disturbance frequency and intensity that had equivalent long-term negative impacts on experimental communities. Our results show that an increase in disturbance intensity is a bigger threat for biodiversity and biomass recovery than the occurrence of more frequent but less intense disturbances.

To evaluate the effects of meltwater discharge from marine-terminating glaciers on a fjord protist community in northwestern Greenland during summer, we investigated the distribution, abundance and biomass of the protist community and their relationships with hydrographic parameters. In the standing stock of protists, dinoflagellates (46.4%) and oligotrich ciliates (39.5%) were dominant throughout the study region. With respect to vertical distribution, oligo - trich ciliates were abundant in the surface layer, mainly due to suitable food conditions (abundance of diatom and nanoflagellates). Near glaciers, relatively high chlorophyll a (chl a) concentrations were found in the subsurface layers associated with the low-temperature, high-turbidity and slightly high nutrient levels, indicating that the nutrient inputs from the upwelling glacialmeltwater plume increased primary production. Large-sized Protoperidium spp. were found only at stations near glaciers where nutrients were abundant, and heterotrophic dinoflagellates showed strong relationships with nanoflagellates. These findings suggest that the upwelling associated with subglacialmeltwater discharge can stimulate nanoflagellate production, resulting in increases in ciliate and heterotrophic dinoflagellate production.

Phagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.

Lake Kislo-Sladkoe is a stratified water body partly isolated from the White Sea. Perennial meromixis in the lake irregularly alternates with mixing events. Taking into account that the protists of Arctic coastal stratified water bodies are understudied, we evaluated for the first time the vertical structure, species richness, and diversity of protists assigned to different taxonomic groups in Lake Kislo-Sladkoe using light, luminescent, and scanning electron microscopy. To test the research hypothesis that a mixing event affects the vertical stratification and species composition of protists in a stratified lake, we compared the protist communities of Lake Kislo-Sladkoe in two extremely different states: strong meromixis vs. full vertical mixing. A total of 97 morphologically distinct phototrophic, heterotrophic, and mixotrophic protists were revealed with the most diverse supertaxa SAR (59), Obazoa (9), and Excavates (14). The hidden diversity of protists (43 species) was a bit less than the active diversity (54 species). A taxonomic list and micrographs of cells for the observed protists are provided. The majority of species revealed are cosmopolitan or widespread in the northern sea waters. The vertical patterns of protist communities were absolutely different in 2018 and 2021. In July 2018, clearly distinct protist communities inhabited different layers of the lake. Bloom of cryptophyte Rhodomonas cf. baltica was detected in chemocline, whereas the maximum density of its grazers was observed in adjacent layers, mainly dinoflagellates Gymnodinium sp. and Scrippsiella trochoidea, as well as a ciliate Prorodon sp. In 2021 due to the recent mixing of lake and seawater, there were no distinct communities in the water column except the superficial 0–1 m layer of fresh water.

Background The temperate grasslands are facing numerous pressures from global change. Despite their essential ecological and economic role, how their microbial communities react to multiple varying factors remain obscure. In this study, we simulated three global change drivers, i.e., nitrogen deposition (ambient N vs. elevated N, aN vs. eN), precipitation increase (ambient precipitation vs. elevated precipitation, aP vs. eP), and mowing, represented experimentally by clipping (unclipped vs. clipped, uC vs. CL), together in all possible combinations in a temperate semi-arid grassland ecosystem. Results Nitrogen addition had negative effects on the richness of bacterial and fungal communties, significantly changed their structures ( P  < 0.05) and increased their dissimilarities ( P  < 0.05), while water addition had positive effects on fungal and protist communities and significantly stimulated the α-diversity of protist communities under N addition without clipping, which was in contrast to the effect in clipped plots. Clipping had a marginal effect on fungal communities and significantly affected protist communities ( P  < 0.05). A notable interactive effect of N and precipitation on the structure of bacterial communities and a significant interactive effect of clipping and precipitation on protists were found. Combination effects of N with precipitation or clipping on module aggregation of meta-networks were also observed between uC and CL, as well as aP and eP meta-networks. Bacterial, fungal, and protist communities varied in their assembly mechanisms, and their assembly processes differed in response to the three global change factors. Conclusions Overall, N, water addition, and clipping individually and/or interactively, in distinct degrees, altered soil microbial interaction, community structure, and the potential function in a semi-arid steppe. These findings enhance our understanding of soil microbial community assembly and provide a scientific basis for managing temperate grasslands, particularly in the context of global change's impact on ecosystem function and stability.