Resource heterogeneity structures aquatic bacterial communities

Terrestrial dissolved organic matter inputs drive the temporal dynamics of riverine bacterial ecological networks and assembly processes

Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.

Divergent Fate and Roles of Dissolved Organic Matter from Spatially Varied Grassland Soils in China During Long-Term Biogeochemical Processes

Terrestrial dissolved organic matter (DOM) is critical to global carbon and nutrient cycling, climate change, and human health. However, how the spatial and compositional differences of soil DOM affect its dynamics and fate in water during the carbon cycle is largely unclear. Herein, the biodegradation of DOM from 14 spatially distributed grassland soils in China with diverse organic composition was investigated by 165 days of incubation experiments. The results showed that although the high humified fraction (high-HS) regions were featured by high humic-like fractions of 4-25 kDa molecular weight, especially the abundant condensed aromatics and tannins, they unexpectedly displayed greater DOM degradation during 45-165 days. In contrast, the unique proteinaceous and 25-100 kDa fractions enriched in the low humified fraction (low-HS) regions were drastically depleted and improved the decay of bulk DOM but only during 0-45 days. Together, DOM from the high-HS regions would cause lower CO2 outgassing to the atmosphere but higher organic loads for drinking water production in the short term than that from the low-HS regions. However, this would be reversed for the two regions during the long-term transformation processes. These findings highlight the importance of spatial and temporal variability of DOM biogeochemistry to mitigate the negative impacts of grassland soil DOM on climate, waters, and humans.

Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater

Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.

Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes

Understanding the rapid responses of marine microbiomes to environmental disturbances is paramount for supporting early assessments of harm to high-value ecosystems, such as coral reefs. Yet, management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing was applied in conjunction with propidium monoazide for cell-viability assessment as a sensitive tool to determine taxon- and community-level changes in a seawater microbial community under copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the effects of copper on microbial composition, diversity, and richness for the purpose of estimating microbiome Hazard Concentration (mHCx) values. Predicted mHC5 values at which a 5 % change in microbial composition, diversity, and richness occurred were 1.05, 0.72, and 0.38 μg Cu L-1, respectively. Threshold indicator taxa analysis was applied across the copper concentrations to identify taxon-specific change points for decreasing taxa. These change points were then used to generate a Prokaryotic Sensitivity Distribution (PSD), from which mHCxdec values were derived for copper, suitable for the protection of 99, 95, 90, and 80 % of the marine microbiome. The mHC5dec guideline value of 0.61 μg Cu L-1, protective of 95 % of the marine microbial community, was lower than the equivalent Australian water quality guideline value based on eukaryotic organisms at higher trophic levels. This suggests that marine microbial communities might be more vulnerable, highlighting potential insufficiencies in their protection against copper pollution. The mHCx values proposed here provide approaches to quantitatively assess the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines.

Contrasting Effects of Leaf Litter Quality and Diversity on Oviposition of Mosquitoes

The quality and diversity of leaf litter are important variables in determining the availability of energy in detritus-based food webs. These factors can be represented by the stoichiometric proportion between carbon and multiple nutrients, and the mixture of litter from different taxonomic and/or functional origins. In aquatic ecosystems, factors that accelerate litter decomposition can influence the secondary productivity of planktonic microbiota, which act as a link between litter and higher trophic levels. This study aimed to analyze the influence of litter quality and diversity on the oviposition behavior of medically important mosquitoes. We hypothesized that both factors would have a positive effect on the attraction of female mosquitoes and would stimulate a greater amount of oviposition. To test this hypothesis, microcosms containing isolated leaf litter leachates from four plant species were used to manipulate gradients of litter quality, and microcosms with all leachates combined were used to test the effects of litter diversity. The results showed a positive effect of litter quality (p < 0.05) on mosquito oviposition rate, with lower C:P ratio litter species (high-quality litter) presenting higher oviposition rates than litter species with high C:P ratios (low-quality litter). However, contrary to our expectations, litter diversity had a negative effect (p = 0.002) on the magnitude of egg-laying by mosquitoes. Our results highlight the importance of litter quality and diversity for insect reproductive behavior. Our data shows that litter quality can serve as a crucial indicator of a suitable environment utilized by female mosquitoes for oviposition. This finding can enhance our ability to understand and develop effective methods for mitigating the reproduction of medically significant mosquitoes, whether by allowing us to predict, based on the composition of vegetation species, areas more prone to mosquito infestation, or by using high-quality litter in oviposition traps. Furthermore, maintaining vegetation diversity can help control mosquito reproduction.

Statistical prediction of microbial metabolic traits from genomes

The metabolic activity of microbial communities is central to their role in biogeochemical cycles, human health, and biotechnology. Despite the abundance of sequencing data characterizing these consortia, it remains a serious challenge to predict microbial metabolic traits from sequencing data alone. Here we culture 96 bacterial isolates individually and assay their ability to grow on 10 distinct compounds as a sole carbon source. Using these data as well as two existing datasets, we show that statistical approaches can accurately predict bacterial carbon utilization traits from genomes. First, we show that classifiers trained on gene content can accurately predict bacterial carbon utilization phenotypes by encoding phylogenetic information. These models substantially outperform predictions made by constraint-based metabolic models automatically constructed from genomes. This result solidifies our current knowledge about the strong connection between phylogeny and metabolic traits. However, phylogeny-based predictions fail to predict traits for taxa that are phylogenetically distant from any strains in the training set. To overcome this we train improved models on gene presence/absence to predict carbon utilization traits from gene content. We show that models that predict carbon utilization traits from gene presence/absence can generalize to taxa that are phylogenetically distant from the training set either by exploiting biochemical information for feature selection or by having sufficiently large datasets. In the latter case, we provide evidence that a statistical approach can identify putatively mechanistic genes involved in metabolic traits. Our study demonstrates the potential power for predicting microbial phenotypes from genotypes using statistical approaches.

Climate Warming-Driven Changes in the Molecular Composition of Soil Dissolved Organic Matter Across Depth: A Case Study on the Tibetan Plateau

Dissolved organic matter (DOM) is critical for soil carbon sequestration in terrestrial ecosystems. DOM molecular composition varies with soil depth. However, the spatial heterogeneity of depth-dependent DOM in response to climate warming remains unclear, especially in alpine ecosystems. In this study, the DOM of alpine meadow soil samples was characterized comprehensively by using spectroscopy and mass spectrometry, and open-top chambers (OTCs) were employed to simulate warming. It was found that climate warming had the greatest impact on the upper layer (0-30 cm), followed by the lower layer (60-80 cm), while the middle layer (30-60 cm) was the most stable among the three soil layers. The reasons for the obvious changes in DOM in the upper and lower layers of soil were further explained based on biotic and abiotic factors. Specifically, soil nutrients (NH4+-N, NO3--N, TC, and TP) affected the molecular composition of DOM in layer L1 (0-15 cm), while pH affected layer L5 (60-80 cm). Gemmatimonadetes, Proteobacteria, and Actinobacteria played important roles in the composition of DOM in the L5 layer (60-80 cm), while the dominant fungal groups affecting the DOM composition increased in the L1 layer (0-15 cm) under warming. In summary, this research has contributed to a deeper understanding of depth-dependent changes in DOM molecular composition in alpine ecosystems.

The effects of climate warming on microbe-mediated mechanisms of sediment carbon emission

Due to significant differences in biotic and abiotic properties of soils compared to those of sediments, the predicted underlying microbe-mediated mechanisms of soil carbon emissions in response to warming may not be applicable for estimating similar emissions from inland water sediments. We addressed this issue by incubating different types of sediments, (including lake, small river, and pond sediments) collected from 36 sites across the Yangtze River basin, under short-term experimental warming to explore the effects of climate warming on sediment carbon emission and the underlying microbe-mediated mechanisms. Our results indicated that under climate warming CO₂ emissions were affected more than CH₄ emissions, and that pond sediments may yield a greater relative contribution of CO₂ to total carbon emissions than lake and river sediments. Warming-induced CO₂ and CH₄ increases involve different microbe-mediated mechanisms; Warming-induced sediment CO₂ emissions were predicted to be directly positively driven by microbial community network modularity, which was significantly negatively affected by the quality and quantity of organic carbon and warming-induced variations in dissolved oxygen, Conversely, warming-induced sediment CH₄ emissions were predicted to be directly positively driven by microbial community network complexity, which was significantly negatively affected by warming-induced variations in pH. Our findings suggest that biotic and abiotic drivers for sediment CO₂ and CH₄ emissions in response to climate warming should be considered separately when predicting sediment organic carbon decomposition dynamics resulting from climate change.

Dissolved organic matter defines microbial communities during initial soil formation after deglaciation

Ecosystem succession and pedogenesis reshuffle the composition and turnover of dissolved organic matter (DOM) and its interactions with soil microbiome. The changes of these connections are especially intensive during initial pedogenesis, e.g. in young post-glacial areas. The temporal succession and vertical development of DOM effects on microbial community structure remains elusive. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS), high-throughput sequencing, and molecular ecological networks, we characterized the molecular diversity of water-extractable DOM and identified its links to microbial communities in soil profiles along deglaciation chronosequence (12, 30, 40, 52, 80, and 120 years) in the southeastern Tibetan Plateau. Low-molecular-weight compound content decreased, whereas the mid- and high-molecular-weight compounds increased with succession age and soil depth. This was confirmed by the increase in double bond equivalents and averaged oxygen-to‑carbon ratios (O/C), and decrease in hydrogen-to‑carbon ratios (H/C), which reflect DOM accumulation and stabilization. Microbial community succession shifted towards the dominance of oligotrophic Acidobacteria and saprophytic Mortierellomycota, reflecting the increase of stable DOM components (H/C < 1.5 and wider O/C). Less DOM-bacterial positive networks during the succession reduced specialization of labile DOM production (such as lipid- and protein-like compounds), whereas more DOM-fungal negative networks increased specialization of stable DOM decomposition (such as tannin- and condensed aromatic-like compounds). Consequently, DOM stability is not intrinsic during initial pedogenesis: stable DOM compounds remain after fast bacterial utilization of labile DOM compounds, whereas fungi decompose slowly the remaining DOM pools.

Sunlight irradiation promotes both the chemodiversity of terrestrial DOM and the biodiversity of bacterial community in a subalpine lake

Alpine lake habitats are evolving into subalpine lakes under the scenario of climate change, where the vegetation are promoted due to increasing temperature and precipitation. The abundant terrestrial dissolved organic matter (TDOM) leached from watershed soil into subalpine lakes would undergo strong photochemical reaction due to the high altitude, with the potential to alter DOM composition and affect the bacterial communities. To reveal the transformation of TDOM by both photochemical and microbial processes in a typical subalpine lake, Lake Tiancai (located 200 m below the tree line) was chosen. TDOM was extracted from the surrounding soil of Lake Tiancai and then subjected to the photo/micro-processing for 107 days. The transformation of TDOM was analyzed by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and fluorescence spectroscopy, and the shift of bacterial communities was analyzed using 16s rRNA gene sequencing technology. Dissolved organic carbon and light-absorbing components (a₃₅₀) decay accounted for approximately 40% and 80% of the original, respectively, in the sunlight process, but both less than 20% in the microbial process for 107 days. The photochemical process promoted the chemodiversity as there were ∼7000 molecules after sunlight irradiation, compared to ∼3000 molecules in the original TDOM. Light promoted the production of highly unsaturated molecules and aliphatics, which were significantly associated with Bacteroidota, suggesting that light may influence bacterial communities by regulating the DOM molecules. Carboxylic-rich alicyclic molecules were generated in both photochemical and biological processes, suggesting TDOM was converted to a stable pool over time. Our finding on the transformation of terrestrial DOM and the alternation of bacterial community under the simultaneously photochemical and microbial processes will help to reveal the response of the carbon cycle and lake system structure to climate change for high-altitude lakes.

Chemodiversity of Dissolved Organic Matter Is Governed by Microbial Biogeography in Inland Waters

Dissolved organic matter (DOM) is crucial for the carbon biogeochemical cycle and has a close link with microbiome in aquatic ecosystems; however, the causal relationship between DOM and microbial diversity in inland waters is not very clear so far. Therefore, a national survey of China's inland waters was conducted, and the DOM chemical composition and microbial community composition were determined by Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing to clarify the abovementioned question. Here, we found that DOM chemodiversity was governed by microbial community assembly in inland waters, not vice versa. Under the control of microbial biogeography, DOM chemodiversity showed a clear geographical distribution difference. Water DOM chemodiversity was mainly constrained by bacterial and archaeal community composition, whereas sediment DOM chemodiversity was mainly controlled by eukaryotic and fungal community composition. In addition, the sediment DOM chemical composition was also affected by the interaction of different microbial groups between waters and sediments. The study is the first to clarify the causal relationship and proposes a microbial regulatory mechanism on the geographical distribution pattern of DOM chemodiversity, thus further deepening the understanding of the DOM biogeochemical cycle.

Urbanization influenced the interactions between dissolved organic matter and bacterial communities in rivers

Increased urbanization and anthropogenic activities can alter dissolved organic matter (DOM) and complicate its interaction with bacteria in rivers' ecosystems, however, there is limited information about how bacterial communities respond to DOM components in rivers with different urbanization levels. Here, we combined spectroscopy-based DOM analysis and 16S rRNA gene amplicon sequencing to investigate the associations of bacterial taxa and DOM properties as well as the impacts of DOM on bacterial niche breadth in North River (NR) and West River (WR) of Jiulong River watershed, southern China, which had low and high urbanization levels, respectively. Spectroscopy analysis showed that hydrophilic DOM was predominant in both rivers whereas chromophoric DOM was higher in WR. Network analysis indicated that only seven bacterial genera (i.e., hg clade, chthoniobacter, Geobacter, Acidibacter, Alphal Cluster, Fluviicola, and Lacunisphaera) showed strong associations with DOM optical variables in both rivers, whereas more than 85% of DOM-bacterial genera associations were different between rivers. These results suggest that the relationship between DOM and bacterial communities had different responses in rivers with different urbanization levels. The partial least square path model indicated that the total standardized effect of physico-chemicals on bacterial niche breadth was higher in NR (0.62) than in WR (0.35), whereas humic substances showed an opposite pattern (NR: -0.42; WR: 1.67). The distinct effects of physico-chemicals and DOM on bacterial niche breadths between rivers could be due to the different effects of urbanization and human activities on the environmental conditions of riverine ecosystems. Our findings revealed a huge dissimilarity in the bacteria-DOM co-occurrence networks between rivers with different urbanization levels and provide a novel insight that urbanization may enhance DOM's importance to bacterial niche breadths.

Spatial and temporal dynamic response of abundant and rare aerobic denitrifying bacteria to dissolved organic matter in natural water: A case study of Lake Baiyangdian, China

Revealing the responses of abundant and rare aerobic denitrifying bacteria to dissolved organic matter (DOM) composition is essential for understanding the aquatic N cycle ecosystems. In this study, fluorescence region integration and high-throughput sequencing techniques were used to investigate the spatiotemporal characteristics and dynamic response of DOM and aerobic denitrifying bacteria. The DOM compositions were significantly different among the four seasons (P < 0.001) without spatial differences. Tryptophan-like substances (P2, 27.89-42.67%) and microbial metabolites (P4, 14.62-42.03%) were the dominant components, and DOM exhibited strong autogenous characteristics. Abundant (AT), moderate (MT), and rare taxa (RT) of aerobic denitrifying bacteria showed significant and spatiotemporal differences (P < 0.05). The responses of α-diversity and niche breadth of AT and RT to DOM differed. The DOM explanation proportion for aerobic denitrifying bacteria exhibited spatiotemporal differences based on redundancy analysis. Foliate-like substances (P3) had the highest interpretation rate of AT in spring and summer, while humic-like substances (P5) had the highest interpretation rate of RT in spring and winter. Network analysis showed that RT networks were more complex than AT networks. Pseudomonas was the main genus associated with DOM in AT on a temporal scale, and was more strongly correlated with tyrosine-like substances (P1), P2, and P5. Aeromonas was the main genus associated with DOM in AT on a spatial scale and was more strongly correlated with P1 and P5. Magnetospirillum was the main genus associated with DOM in RT on a spatiotemporal scale, which was more sensitive to P3 and P4. Special operational taxonomic units were transformed between AT and RT with seasonal changes, but not between the two regions. To summarize, our results revealed that bacteria with different abundances utilized DOM components differently, and provides new insight on the spatiotemporal response of DOM and aerobic denitrifying bacteria in aquatic ecosystems of biogeochemical significance.

Interactions between dissolved organic matter and the microbial community are modified by microplastics and heat waves

Dissolved organic matter (DOM) exists widely in natural waters and plays an important role in river carbon cycles and greenhouse gas emissions through microbial interactions. However, information on DOM-microbe associations in response to environmental stress is limited. River environments are the main carriers of microplastic (MP) pollution, and global heat waves (HWs) are threatening river ecology. Here, through MP exposure and HW simulation experiments, we found that DOM molecular weight and aromaticity were closely related to initial microbial communities. Moreover, MP-derived DOM regulated microbial community abundance and diversity, influenced microorganism succession trajectories as deterministic factors, and competed with riverine DOM for microbial utilization. SimulatedHWs enhanced the MP-derived DOM competitive advantage and drove the microbial community to adopt a K-strategy for effective recalcitrant carbon utilization. Relative to single environmental stressor exposure, combined MP pollution and HWs led to a more unstable microbial network. This study addresses how MPs and HWs drive DOM-microbe interactions in rivers, contributes to an in-depth understanding of the fate of river DOM and microbial community succession processes, and narrows the knowledge gap in understanding carbon sinks in aquatic ecosystems influenced by human activities and climate change.

Integrative analysis of microbiome and metabolome reveals the linkage between gut microbiota and carp growth

Gut microbiota and their metabolites are increasingly recognized for their crucial role in regulating the health and growth of the host. The mechanism by which the gut microbiome affects the growth rate of fish (Cyprinus carpio) in the rice-fish coculture system, however, remains unclear. In this study, the gut contents of the fast-growing and slow-growing (FG and SG) carp were collected from the rice-fish coculture system for both the fish gut microbiome and metabolome analyses. High throughput 16 S rRNA gene sequencing showed that the overall gut microbiota of FG group was distinct from that of SG group. For example, the cyanobacteria were highly enriched in the guts of SG carp (18.61%), in contrast, they only represented a minor fraction of gut microbiota for FG group (<0.20%). The liquid chromatography-mass spectrometry (LC-MS)-based metabolomics analysis revealed that 191 identified metabolites mostly located in 18 KEGG pathways were differentially present between the two groups, of which more than 50% of these metabolites were involved in lipid and amino acids metabolism. Compared with the FG group, the gut microbiota of SG group significantly enriched the metabolic pathways involved in the steroid (hormone) biosynthesis, whereas reducing those associated with beta-alanine metabolism, biosynthesis of unsaturated fatty acids and bile secretion. The enrichment and depletion of these metabolic pathways resulted in an increase in steroid metabolites and a decrease in the concentration of spermidine, which may have a major impact on the growth rate of carp. The metabolome results were further supported by the predicated KEGG functions of the gut microbiomes of the two groups, pointing out that the gut microbiota could substantially affect the growth of fish via their unique metabolic functions. Together, our integrated fish gut microbiome and metabolome analysis has substantial implications for the development of engineered microbiome technologies in aquaculture.

High carbon resource diversity enhances the certainty of successful plant pathogen and disease control

The host-associated microbiome highly determines plant health. Available organic resources, such as food for microbes, are important in shaping microbial community structure and multifunctionality. However, how using organic resources precisely manipulates the soil microbiome and makes it supportive of plant health remains unclear. Here, we experimentally tested the influence of carbon resource diversity on the microbial trophic network and pathogen invasion success in a microcosm study. We further explored how resource diversity affects microbial evenness, community functions, and plant disease outcomes in systems involving tomato plants and the in vivo soil microbiome. Increasing available resource diversity altered trophic network architecture, increased microbial evenness, and thus increased the certainty of successful pathogen control. By contrast, the invasion resistance effects of low resource diversity were less effective and highly varied. Accordingly, increases in the evenness and connection of dominant species induced by high resource diversity significantly contributed to plant disease suppression. Furthermore, high carbohydrate diversity upregulated plant immune system regulation-related microbial functions. Our results deepen the biodiversity-invasion resistance theory and provide practical guidance for the control of plant pathogens and diseases by using organic resource-mediated approaches, such as crop rotation, intercropping, and organic amendments.

Composition of dissolved organic matter (DOM) in wastewater treatment plants influent affects the efficiency of carbon and nitrogen removal

Wastewater treatment plants (WWTPs) play a critical role in receiving, removing, and discharging dissolved organic matter (DOM) in aquatic systems. To date, understanding the composition and fate of DOM in different WWTPs with various environmental and socioeconomic conditions is limited. This study analyzed DOM components in the influent and effluent samples from 49 WWTPs in China using EEM-PARAFAC and ESI-FT-ICR-MS methods. The influencing factors of DOM components in the influent were also analyzed. Geographic location and GDP showed significant (p < 0.05) correlations with DOM components in the influent. The removal efficiency of DOM in WWTPs was closely related to the DOM compositions, where carbohydrates, lipids, and protein-like components (removal efficiencies > 75 %) were more readily decomposed than the humic-like components, lignin, and tannin. The relative fraction of humic-like compound C3 in the influent was correlated negatively with total nitrogen (TN) and chemical oxygen demand (COD) removal in WWTPs (p < 0.05). Besides, the relative fraction of DOM containing the element sulfur also showed significant negative correlations with the humification of DOM (p < 0.05). The results from EEM-PARAFAC and ESI-FT-ICR-MS methods showed no obvious correlation for the DOM characterizations except for humic-like fluorescent fraction C3 and lignin, while significant positive correlations (p < 0.05) between the aromatic index (AI_mod) from the ESI-FT-ICR-MS analysis and the humification index (HIX) from spectrofluorimetry. This supports the use of these spectral indexes as simple surrogates to represent part chemical compositions in further research.

The ephemeral resource patch concept

Ephemeral resource patches (ERPs) - short lived resources including dung, carrion, temporary pools, rotting vegetation, decaying wood, and fungi - are found throughout every ecosystem. Their short-lived dynamics greatly enhance ecosystem heterogeneity and have shaped the evolutionary trajectories of a wide range of organisms - from bacteria to insects and amphibians. Despite this, there has been no attempt to distinguish ERPs clearly from other resource types, to identify their shared spatiotemporal characteristics, or to articulate their broad ecological and evolutionary influences on biotic communities. Here, we define ERPs as any distinct consumable resources which (i) are homogeneous (genetically, chemically, or structurally) relative to the surrounding matrix, (ii) host a discrete multitrophic community consisting of species that cannot replicate solely in any of the surrounding matrix, and (iii) cannot maintain a balance between depletion and renewal, which in turn, prevents multiple generations of consumers/users or reaching a community equilibrium. We outline the wide range of ERPs that fit these criteria, propose 12 spatiotemporal characteristics along which ERPs can vary, and synthesise a large body of literature that relates ERP dynamics to ecological and evolutionary theory. We draw this knowledge together and present a new unifying conceptual framework that incorporates how ERPs have shaped the adaptive trajectories of organisms, the structure of ecosystems, and how they can be integrated into biodiversity management and conservation. Future research should focus on how inter- and intra-resource variation occurs in nature - with a particular focus on resource × environment × genotype interactions. This will likely reveal novel adaptive strategies, aid the development of new eco-evolutionary theory, and greatly improve our understanding of the form and function of organisms and ecosystems.

Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems

BACKGROUND

Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with ¹³CO₂, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP).

RESULTS

Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem.

CONCLUSIONS

Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems. Video abstract.

High stability of autochthonous dissolved organic matter in karst aquatic ecosystems: Evidence from fluorescence

Biological carbon pump (BCP) in karst areas has received intensive attention for years due to their significant contribution to the global missing carbon sink. The stability of autochthonous dissolved organic matter (Auto-DOM) produced by BCP in karst aquatic ecosystems may play a critical role in the missing carbon sink. However, the source of dissolved organic matter (DOM) in inland waters and its consumption by planktonic bacteria have not been thoroughly examined. Recalcitrant dissolved organic matter (RDOM) may exist in karst aquatic ecosystem as in the ocean. Through the study of the chromophoric dissolved organic matter (CDOM) and the interaction between CDOM and the planktonic bacterial community under different land uses at the Shawan Karst Water-carbon Cycle Test Site, SW China, we found that C2, as the fluorescence component of Auto-DOM mineralised by planktonic bacteria, may have some of the characteristics of RDOM and is an important DOM source in karst aquatic ecosystems. The stability ratio (Fmax_(C2/(C1+C2))) of Auto-DOM reached 89.6 ± 6.71% in winter and 64.1 ± 7.19% in spring. Moreover, correlation-based network analysis determined that the planktonic bacterial communities were controlled by different fluorescence types of CDOM, of which C1 (fresh Auto-DOM), C3 (conventional allochthonous DOM (Allo-DOM)) and C4 (the Allo-DOM mineralised by bacteria) were clustered in one module together with prevalent organic-degrading planktonic bacteria; C2 was clustered in another tightly combined module, suggesting specific microbial utilization strategies for the C2 component. In addition, some important planktonic bacterium and functional genes (including chemotrophic heterotrophs and photosynthetic bacteria) were found to be affected by high Ca²⁺ and dissolved inorganic carbon (DIC) concentrations in karst aquatic ecosystems. Our research showed that Auto-DOM may be as an important carbon sink as the Allo-DOM in karst ecosystems, the former generally being neglected based on a posit that it is easily and first mineralized by planktonic bacteria.

Ecological networks of dissolved organic matter and microorganisms under global change

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions.

Microbes are intimately linked with the fate of organic matter. Here the authors develop an ecological network framework and show how microbes and dissolved organic matter interact along global change drivers of temperature and nutrient enrichment via manipulative field experiments on mountains.

Insight into the effect of wastewater-derived dissolved organic matter composition on norgestrel degradation in activated sludge: Coupled bacterial community and molecular characteristics

Dissolved organic matter (DOM) mediates the microbial transformation of micropollutants, including norgestrel (NGT) in natural waters. However, little is known of the effect of complex and variable wastewater-derived DOM composition on NGT degradation during wastewater treatment. In this study, the relationship between the compositions of initial DOM and NGT removal efficiencies of 17 wastewater treatment plants (WWTPs) in spring and summer were analyzed. The different molecular composition of DOM was selected in the lab to further explore its effect on NGT degradation by activated sludge. Results indicated that the DOM composition was a substantial driver of NGT removal in WWTPs. The discrepancies in the initial DOM composition contributed to the differences in the kinetics of NGT degradation by activated sludge. The larger rapid decay phase rates of NGT are usually accompanied by a large proportion of labile substances in DOM. High-throughput sequencing and ultrahigh-resolution mass spectrometry were used to further analyze the evolution of bacterial communities and DOM molecular composition were combined with network analysis to reveal the intrinsic relationship that how DOM composition affected NGT degradation by regulating core microbes. Eighty-nine core OTUs were significantly associated with NGT degradation, and 73 occurred in the rapid decay phase, implying that NGT degradation was mainly regulated by the initial composition of DOM. Nine major transformation products were identified in different groups with widely varying concentrations or relative abundances of these transformation products. This work provides valuable insights into the effects of wastewater-derived DOM composition on NGT degradation by activated sludge and innovatively explores the influence mechanisms from the bacterial community and molecular characterization perspectives.

Properties of sediment dissolved organic matter respond to eutrophication and interact with bacterial communities in a plateau lake

Sediment dissolved organic matter (DOM) in inland waters is commonly affected by environmental changes. However, knowledge about how sediment DOM responds to eutrophication and the associations between sediment DOM and bacterial communities requires further investigation. We selected a sediment core from Dianchi Lake (China) that was dated from 1864 to 2019 by the activity of radionuclides (²¹⁰Pb and ¹³⁷Cs). δ¹³C_DOC changes fit well with the historical record that heavy eutrophic status in Dianchi Lake were observed since 1980s. Large amounts of dissolved organic carbon (DOC), chromophoric (CDOM) and fluorescent (FDOM) DOM accumulated at the top of the sediments during the eutrophication period (1982-present). The additional algae sources with a higher degradation rate altered the composition, aromaticity and humification of DOM. After long-term mineralization, the remaining DOM became more and more recalcitrant and kept a relatively stable level at older sediments. A co-occurrence network analysis revealed that Proteobacteria, Chloroflexi, Acidobacteriota, Bacteroidota and Desulfobacterota were the most abundant species at the phylum level and clustered into three primary modules. Different microbes shared unique preferences for niches, causing a heterogeneous bacterial distribution at different depths. We conducted Spearman's correlation and redundancy analysis (RDA) to explore potential interactions between bacterial community and sediment DOM. The richness and diversity of bacterial communities were positively related to DOM content, suggesting abundant DOM can produce more available resources for bacteria. RDA results showed some specific species might modify DOM composition and structure. This study suggests that sediment DOM properties were regulated by source transformation during eutrophication, and emphasizes the importance of microbial role on sediment biogeochemical process.

Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation

The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.

Overlying water fluoride concentrations influence dissolved organic matter composition and migration from pore water in sediment via bacterial mechanisms

Fluoride (F^-) is widespread in aquatic environments; however, it is not clear whether the fluctuation of F^- concentrations in overlying lake water affects the composition and migration of dissolved organic matter (DOM) from sediment. A case study was presented in Sand Lake, China, and an experiment was conducted to analyze the influence of different F^- concentrations in overlying water on DOM characteristics. Diffusion resulted in similarities in DOM components between overlying and pore waters, and bacterial activities and enzyme variation resulted in differences between them. Higher F^- concentrations in overlying water resulted in a higher pH of pore water, which favored the enrichment of protein-like substances. Higher F^- concentrations caused lower DOM concentrations and lower maximum fluorescence intensities (F_max) of protein-like components in pore water. The F^- concentrations had significantly negative correlations with Shannon indexes (P < 0.05). Thiobacillus influenced the migration of tyrosine-like substances by decreasing the pH of pore water. Trichococcus and Fusibacter altered the F_max of protein-like, humic-like, and fulvic-like substances. The F^- concentrations affected the DOM composition and migration due to the response of functional bacterial communities, which were positively correlated with the relative abundance of Thiobacillus and negatively correlated with the relative abundances of Trichococcus and Fusibacter. The high F^- concentrations influenced the biosynthesis and degradation of protein-like substances by shifting the abundances of the relevant enzymes. The results of this study may provide ideas for investigating DOM cycling under the influence of F^-, especially in lakes with fluctuations in F^- concentrations.

Diversity and distribution of sediment bacteria across an ecological and trophic gradient

The microbial communities of lake sediments have the potential to serve as valuable bioindicators and integrators of watershed land-use and water quality; however, the relative sensitivity of these communities to physio-chemical and geographical parameters must be demonstrated at taxonomic resolutions that are feasible by current sequencing and bioinformatic approaches. The geologically diverse and lake-rich state of Minnesota (USA) is uniquely situated to address this potential because of its variability in ecological region, lake type, and watershed land-use. In this study, we selected twenty lakes with varying physio-chemical properties across four ecological regions of Minnesota. Our objectives were to (i) evaluate the diversity and composition of the bacterial community at the sediment-water interface and (ii) determine how lake location and watershed land-use impact aqueous chemistry and influence bacterial community structure. Our 16S rRNA amplicon data from lake sediment cores, at two depth intervals, data indicate that sediment communities are more likely to cluster by ecological region rather than any individual lake properties (e.g., trophic status, total phosphorous concentration, lake depth). However, composition is tied to a given lake, wherein samples from the same core were more alike than samples collected at similar depths across lakes. Our results illustrate the diversity within lake sediment microbial communities and provide insight into relationships between taxonomy, physicochemical, and geographic properties of north temperate lakes.

Particle foraging strategies promote microbial diversity in marine environments

Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.

Bacterioplankton Zonation Does Exist in High Elevation, Polymictic Lakes

The assessment of distribution patterns or zonation of planktonic microbes along the water column is a crucial step to interpret their function in the ecosystem. In lakes without seasonal thermal stratification or polymictic systems such as high elevation tropical lakes, planktonic bacterial taxa are probably homogeneously distributed in the water column in contrast to what is known for thermally stratified lakes. However, we know little about bacterial distribution patterns in polymictic lakes and their relation to environmental gradients other than temperature. Here we assessed the diversity, microdiversity, and bacterial community composition at different discrete depths in three high elevation lakes (4,400-4,550 m above sea level) from the Andean plateau to test whether bacterial zonation patterns exist along the water column. For this objective, we analyzed bulk DNA and the putatively active fraction (cDNA) of the 16S rRNA gene. Although a clear gradient of temperature and oxygen was not detected along the water column, a significant vertical spatial zonation of the bacterial communities was present in two out of the three lakes, with microdiversity contributing to such pattern. Our results provide a reference for understanding how changing environmental conditions could affect high elevation aquatic ecosystems, particularly when warming is amplified with elevation, accelerating changes in hydrological regimes and biodiversity. Finally, our results highlight the importance of incorporating the whole water column in ecological studies of aquatic ecosystems lacking temporal or permanent thermal stratification.

Effects of bioturbation by tubificid worms on biogeochemical processes, bacterial community structure and diversity in heterotrophic wetland sediments

Bioturbation activity of tubificid worms has been recognized as a key process influencing organic matter processing and nutrient cycling in benthic aquatic ecosystems. This activity is expected to modify benthic microbial communities by affecting the physical and chemical environment in sediments. Nevertheless, quantifications of bacterial community changes associated with bioturbation in freshwater ecosystems are still lacking. The present study aimed at evaluating the impact of tubificid worms on bacterial community structure using NGS approach (16S metabarcoding) and long (6 months) laboratory experiments on four heterotrophic wetland sediments. Worm bioturbation activity significantly stimulated biogeochemical processes at the water-sediment interface but only had a marginally significant effect on bacterial community structures. Yet, bacterial diversity was consistently reduced in presence of worms. Such decrease could be associated with the stimulation of organic matter mineralization by worms, leading to a reduction of the diversity of trophic niches available for bacterial species. The slight changes in bacterial community structures induced by bioturbation did not appear to control biogeochemical processes. Thus, the stimulation of biogeochemical processes by worm bioturbation was more associated with a stimulation of the initial bacterial community than with a drastic change in bacterial communities induced by worms.

Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.

Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism

The relationship between the number of available nutrients and community diversity is a central question in ecological research that remains unanswered. Here we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.

Marine dissolved organic matter: a vast and unexplored molecular space

Abstract

Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities.

Key points

• Marine DOM is a vast, unexplored biotechnological resource.

• Untargeted bioscreening approaches are emerging for natural product screening.

• Perspectives for developing bioscreening platforms for marine DOM are discussed.

Biodegradable dissolved organic carbon shapes bacterial community structures and co-occurrence patterns in large eutrophic Lake Taihu

Interactions between dissolved organic matter (DOM) and bacteria are central in the biogeochemical cycles of aquatic ecosystems; however, the relative importance of biodegradable dissolved organic carbon (BDOC) compared with other environmental variables in structuring the bacterial communities needs further investigation. Here, we investigated bacterial communities, chromophoric DOM (CDOM) characteristics and physico-chemical parameters as well as examined BDOC via bioassay incubations in large eutrophic Lake Taihu, China, to explore the importance of BDOC for shaping bacterial community structures and co-occurrence patterns. We found that the proportion of BDOC (%BDOC) correlated significantly and positively with the DOC concentration and the index of the contribution of recent produced autochthonous CDOM (BIX). %BDOC, further correlated positively with the relative abundance of the tryptophan-like component and negatively with CDOM aromaticity, indicating that autochthonous production of protein-like CDOM was an important source of BDOC. The richness of the bacterial communities correlated negatively with %BDOC, indicating an enhanced number of species in the refractory DOC environments. %BDOC was identified as a significant stronger factor than DOC in shaping bacterial community composition and the co-occurrence network, suggesting that substrate biodegradability is more significant than DOC quantity determining the bacterial communities in a eutrophic lake. Environmental factors explained a larger proportion of the variation in the conditionally rare and abundant subcommunity than for the abundant and the rare bacterial subcommunities. Our findings emphasize the importance of considering bacteria with different abundance patterns and DOC biodegradability when studying the interactions between DOM and bacteria in eutrophic lakes.

Magnetic biochar production alters the molecular characteristics and biological response of pyrolysis volatile-derived water-soluble organic matter

The formed Fe oxides (minerals) in the magnetic biochar production process can facilitate its recovery and carbon retention rate. However, the influence of Fe oxides on pyrolysis volatile-derived water-soluble organic matter (PVWSOM, also called wood vinegar) has been largely overlooked. Results demonstrated that in-situ formed Fe oxides (α-Fe₂O₃ and Fe₃O₄) could obviously inhibit biomass cracking and accordingly reduce PVWSOM emissions, as indicated by decreased PVWSOM concentrations from 28.7 to 6.8 mg C/g biomass. FT-ICR MS results further indicated that Fe oxides suppressed the formation of large-molecular-weight PVWSOM compounds with high degree of unsaturation (DBE value > 5) and oxygen content (oxygen number > 5), leading to lower polarity and aromaticity. Therefore, the changes in PVWSOM molecular structures caused by Fe oxides relieved its toxicity on wheat seed growth, and reduced negative impact on soil microbial diversity and promoted soil bacterial Proteobacteria and Acidobacteria. These results indicate that molecular structures of PVWSOM from biomass pyrolysis also can be changed by Fe oxides to affect its application.

Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions

It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.

Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions

Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.

An evolutionary algorithm for designing microbial communities via environmental modification

Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.

Interplay of population size and environmental fluctuations: A new explanation for fitness cost rarity in asexuals

Theoretical models of ecological specialisation commonly assume that adaptation to one environment leads to fitness reductions (costs) in others. However, experiments often fail to detect such costs. We addressed this conundrum using experimental evolution with Escherichia coli in several constant and fluctuating environments at multiple population sizes. We found that in fluctuating environments, smaller populations paid significant costs, but larger ones avoided them altogether. Contrastingly, in constant environments, larger populations paid more costs than the smaller ones. Overall, large population sizes and fluctuating environments led to cost avoidance only when present together. Mutational frequency distributions obtained from whole-genome whole-population sequencing revealed that the primary mechanism of cost avoidance was the enrichment of multiple beneficial mutations within the same lineage. Since the conditions revealed by our study for avoiding costs are widespread, it provides a novel explanation of the conundrum of why the costs expected in theory are rarely detected in experiments.

Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa

The bioavailability of organic matter (OM) to marine heterotrophic bacterioplankton is determined by both the chemical composition of OM and the microbial community composition. In the current study, changes in OM bioavailability were identified at Ocean Station Papa as part of the 2018 Export Processes in the Ocean from Remote Sensing (EXPORTS) field study. Removal rates of carbon (C) in controlled experiments were significantly correlated with the initial composition of total hydrolyzable amino acids, and C removal rates were high when the amino acid degradation index suggested a more labile composition. Carbon remineralization rates averaged 0.19 ± 0.08 μmol C L-1 d-1 over 6-10 days while bacterial growth efficiencies averaged 31 ± 7%. Amino acid composition and tandem mass spectrometry analysis of compound classes also revealed transformations to a more degraded OM composition during experiments. There was a log2-fold increase in the relative abundances of 16S rDNA-resolved bacterioplankton taxa in most experiments by members of the Methylophilaceae family (OM43 genus) and KI89A order. Additionally, when OM was more bioavailable, relative abundances increased by at least threefold for the classes Bacteroidetes (Flavobacteriaceae NS2b genus), Alphaproteobacteria (Rhodobacteraceae Sulfitobacter genus), and Gammaproteobacteria (Alteromonadales and Ectothiorhodospiraceae orders). Our data suggest that a diverse group of bacterioplankton was responsible for removing organic carbon and altering the OM composition to a more degraded state. Elevated community diversity, as inferred from the Shannon-Wiener H index, may have contributed to relatively high growth efficiencies by the bacterioplankton. The data presented here shed light on the interconnections between OM bioavailability and key bacterioplankton taxa for the degradation of marine OM.

Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

Non-additive microbial community responses to environmental complexity

Environmental composition is a major, though poorly understood, determinant of microbiome dynamics. Here we ask whether general principles govern how microbial community growth yield and diversity scale with an increasing number of environmental molecules. By assembling hundreds of synthetic consortia in vitro, we find that growth yield can remain constant or increase in a non-additive manner with environmental complexity. Conversely, taxonomic diversity is often much lower than expected. To better understand these deviations, we formulate metrics for epistatic interactions between environments and use them to compare our results to communities simulated with experimentally-parametrized consumer resource models. We find that key metabolic and ecological factors, including species similarity, degree of specialization, and metabolic interactions, modulate the observed non-additivity and govern the response of communities to combinations of resource pools. Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems.

Resource aromaticity affects bacterial community successions in response to different sources of dissolved organic matter

Microbe-mediated transformation of dissolved organic matter (DOM) contributes substantially to the carbon dynamics and energy flow of aquatic ecosystems; yet, the temporal dynamics of bacterial communities in response to diverse DOM sources are scarcely known. Here, we supplied four distinct sources of DOM (algae-derived, macrophyte-derived, sewage-derived, and soil-derived) to the same bacterial community to track the effects of these DOM sources on the carbon processing and successional dynamics of bacterial communities. Although by the end of the incubation the proportion of bio-degraded DOM was significantly lower in the soil-derived DOM treatment than for the other sources, rapid initial metabolism of protein-like and aliphatic compounds and increasing aromaticity and humification degree of DOM during the incubation period were observed for all sources. The role of stochastic processes in governing the community assembly decreased substantially from 61.4% on the first day to 16.7% at the end of the incubation. Moreover, stronger deterministic selection and lower temporal turnover rate were observed for the soil-derived than the other DOM sources, indicating stronger environmental filtering by the more aromatic DOM. Significant correlations were also observed between the humification index (HIX) of DOM and bacterial community diversities, co-occurrence patterns, habitat niche breadths, and the contribution of deterministic ecological processes. In addition, we demonstrated that taxa with different abundance patterns all play crucial but different roles in the response to DOM variation. Our results indicate the importance of DOM aromaticity as a predictor of the outcome of different DOM sources on bacterial community dynamics.

Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods?

Stormwater infiltration systems (SIS) have been set up to collect and infiltrate urban stormwater runoff in order to reduce flooding and to artificially recharge aquifers. Such practices produce environmental changes in shallow groundwater ecosystems like an increase in organic matter concentrations that could drive changes in structure and functions of groundwater microbial communities. Previous works suggested that SIS influence groundwater physico-chemistry during either rainy and dry period but no study has examined the impact of SIS on groundwater microorganisms during both periods. This study aimed to fill this gap by assessing SIS impacts on groundwater quality parameters in three SIS with vadose zone thickness < 3 m during two contrasting meteorological conditions (rainy/dry periods). Physicochemical (dissolved organic carbon and nutrient concentrations) and microbial variables (biomass, dehydrogenase and hydrolytic activities, and bacterial community structure) were assessed on SIS-impacted and non-SIS-impacted zones of the aquifers for the three SIS. Using clay beads incubated in the aquifer to collect microbial biofilm, we show that SIS increased microbial activities, bacterial richness and diversity in groundwater biofilms during the rainy period but not during the dry period. In contrast, the significant differences in dissolved organic carbon and nutrient concentrations, biofilm biomass and bacterial community structures (Bray-Curtis distances, relative abundances of main bacterial orders) measured between SIS-impacted and non-SIS-impacted zones of the aquifer were comparable during the two periods. These results suggest that structural indicators of biofilm like biomass were probably controlled by long-term effects of SIS on concentrations of dissolved organic matter and nutrients whereas biofilm activities and bacterial richness were temporally stimulated by stormwater runoff infiltrations during the rainy period. This decoupling between the structural and functional responses of groundwater biofilms to stormwater infiltration practices suggests that biofilms functions were highly reactive to fluxes associated with aquifer recharge events.

Blood meal source and mixed blood-feeding influence gut bacterial community composition in Aedes aegypti

BACKGROUND

The guts of blood-sucking insects host a community of bacteria that can shift dramatically in response to biotic and abiotic factors. Identifying the key factors structuring these microbial communities has important ecological and epidemiological implications.

METHODS

We used the yellow fever mosquito, Aedes aegypti, to investigate the impact of mixed blood meals on gut microbiota of vector mosquitoes. Adult females were experimentally fed on sugar or blood from chicken, rabbit or a mixture of chicken and rabbit blood, and their gut microbiota were characterized using 16S rRNA gene amplification and MiSeq sequencing.

RESULTS

The gut bacterial communities of mosquitoes fed on the three blood meal treatments clustered separately, suggesting that host species identity and mixed blood-feeding are key determinants of gut bacterial community composition in mosquitoes. Mixed blood meal had a synergistic effect on both operational taxonomic unit (OTU) richness and the Shannon diversity index, suggesting that mixed blood-feeding can offset the nutritional deficit of blood meals from certain host species. The microbial communities observed in this study were distinct from those identified from similarly fed Ae. aegypti from our previous study.

CONCLUSIONS

These findings demonstrate that vector host-feeding preferences can influence gut microbial composition and diversity, which could potentially impact pathogen acquisition and transmission by the vector. The results also demonstrate that different microenvironmental conditions within the laboratory may play an important role in structuring the microbial communities of independently reared mosquito colonies.

Do bacterioplankton respond equally to different river regulations? A quantitative study in the single-dammed Yarlung Tsangpo River and the cascade-dammed Lancang River

River damming has raised controversial concerns as it simultaneously contributes to socioeconomic development but may jeopardize aquatic ecology. Since bacterioplankton catalyze vital biogeochemical reactions and play important roles in aquatic ecosystems, more attention has been paid to their responses in dammed rivers. Here, a comparative study was conducted between single-dammed (the Yarlung Tsangpo River) and cascade-dammed (the Lancang River) rivers in Southwest China to investigate whether bacterioplankton respond equally to different river regulations. Our results showed that the decreased bacterioplankton abundance and the increased α-diversity always co-occurred in reservoirs of the Yarlung Tsangpo River and the Lancang River. However, the impact of damming on bacterioplankton abundance and α-diversity were resilient in the Lancang River, which can be attributed to the repeated alterations of environmental heterogeneity in cascade damming reaches. Meanwhile, a generalized additive model (GAM) was applied to identify the important drivers affecting bacterioplankton variation. The abundance was influenced by trophic conditions, such as dissolved silicon, while α-diversity was closely related to the microbial dispersal process, such as elevation and distance-from source. And it is also noted that the bacterioplankton dispersal process was interrupted in cascade damming reaches. In addition, based on their important drivers, variations in abundance and α-diversity were also predicted by GAM. As revealed by the quantitative mutual validation between the two rivers, abundance and α-diversity in the cascade-dammed river can be predicted by their response to single-dammed river, suggesting that the impact of cascade damming on bacterioplankton can be pre-assessed by referring to the single stage damming effect. Therefore, our study provides the first trial of quantitative evidence that bacterioplankton do not respond equally to different river regulations, and the impact of cascade damming on bacterioplankton can be predicted based on single stage damming effect, which can contribute to the protection of aquatic ecology in the cascade hydropower development.

A Landscape of Opportunities for Microbial Ecology Research

Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.

Elucidating the Competition between Heterotrophic Denitrification and DNRA Using the Resource-Ratio Theory

Heterotrophic denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two microbial processes competing for two shared resources, namely, nitrate and organic carbon (COD). Their competition has great implications for nitrogen loss, conservation, and greenhouse gas emissions. Nevertheless, a comprehensive and mechanistic understanding of the governing factors for this competition is still lacking. We applied the resource-ratio theory to study this competition and validated the theory with experimental data from continuous cultures reported in the literature. Based on this theory, we revealed that influent COD/N ratio alone was not sufficient to predict the competition outcome as the boundary values for different competition outcomes changed substantially with influent resource concentrations. The stoichiometry of the two processes was determinative for the boundaries, whereas the affinity for the shared resources (K_S), maximum specific growth rate (μ_max) of the two species, and the dilution rate had significant impacts as well but mainly at low influent resource concentrations (e.g., <100 μM nitrate). The presented approach allows for a more comprehensive understanding of the parameters controlling microbial competition. The computational comparison between continuous and batch cultures could explain seemingly conflicting experimental results as to the impact of the COD/N ratio. The results also include testable hypotheses and tools for understanding and managing the fate of nitrate in ecosystems, which could also be applied more widely to other species competing for two shared resources.

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche-driven microbial community assembly processes

Shallow thermokarst ponds are a conspicuous landscape element of the Arctic Siberian tundra with high biogeochemical variability. Little is known about how microbes from the regional species pool assemble into local pond communities and how the resulting patterns affect functional properties such as dissolved organic carbon (DOC) remineralization and greenhouse gas (GHG) turnover. We analysed the pelagic microbiomes of 20 ponds in north‐eastern Siberia in the context of their physico‐chemical properties. Ponds were categorized as polygonal or trough according to their geomorphological origin. The diversity of bacteria and eukaryotic microbes was assessed by ribosomal gene tag sequencing. Null model analysis revealed an important role of stochastic assembly processes within ponds of identical origin, in particular for genotypes only occurring in few systems. Nevertheless, the two pond types clearly represented distinct niches for both the bacterial and eukaryotic microbial communities. Carbon dioxide concentration, indicative of heterotrophic microbial processes, varied greatly, especially in the trough ponds. Methane concentrations were lower in polygonal ponds and were correlated with the estimated abundance of methanotrophs. Thus, the overall functional variability of Arctic ponds reflects the stochastic assembly of their microbial communities. Distinct functional subcommunities can, nevertheless, be related to GHG concentrations.

Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities

Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.

Dormancy dampens the microbial distance-decay relationship

Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of 'seed banks'. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 10⁶ simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.