Connecting through space and time: catchment‐scale distributions of bacteria in soil, stream water and sediment

The role of agricultural drainage, storm-events, and natural filtration on the biogeochemical cycling capacity of aquatic and sediment environments in Lake Erie's drainage basin

Lake Erie is the most at risk of the Great Lakes for degraded water quality due to non-point source pollution caused by agricultural activities in the lake's watershed. The extent and temporal patterns of nutrient loading from these agricultural activities is influenced by the timing of agronomic events, precipitation events, and water flow through areas of natural filtration within the watershed. Downstream impacts of these nutrient loading events may be moderated by the co-loading of functionally relevant biogeochemical cycling microbial communities from agricultural soils. This study quantified loading patterns of these communities from tile drain sources, assessed whether functional communities from agricultural sources influenced downstream microbial functionality, and investigated how distance from agricultural sources, storm events, and areas of natural filtration altered nutrient cycling and nutrient fluxes in aquatic and sediment environments. Water and sediment samples were collected in the Wigle Creek watershed in Ontario, from tile drains through to Lake Erie, from May to November 2021, and microbial nitrogen (N) and phosphorous (P) cycling capacity (quantitative PCR), and nutrient levels were evaluated. Results showed that N and P functional groups were co-loaded with nutrients, with increased loading occurring during storm events and during agricultural activities including fertilization and harvest. Overall functional capacity in the aquatic environment decreased with distance from the agricultural sources and as water transited through natural filtration areas. In contrast, the sediment environment was more resilient to both agricultural disturbances and abiotic factors. This study expands our understanding of when and where different stages of N and P cycling occurs in agriculturally impacted watersheds, and identifies both seasons and regions to target with nutrient mitigation strategies.

Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation

Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.

Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America

A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.

Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.

Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland

The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.

Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau

Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.

Coupled effects of landscape structures and water chemistry on bacterioplankton communities at multi-spatial scales

Bacterioplankton communities in rivers are strongly influenced by the surrounding landscape, yet the relationships between land use and bacterioplankton communities at multi-spatial scales and the mechanisms that shape bacterioplankton communities remain unclear. Here, we collected surface water samples from 14 tributaries of the Yuan River, a secondary tributary of the Yangtze River, which has been heavily impacted by human activities. We characterized the bacterioplankton communities by high-throughput sequencing techniques, and managed to identify the mechanisms governing bacterioplankton community assembly. The results showed that, in general, both landscape compositions and landscape configurations had significant effects on bacterial communities, and the effects were greater at the buffer scale than at the sub-basin scale. Additionally, there was no distinct distance-decay pattern for the effects of landscape structures on bacterial communities from the near-distance (100 m) to the long-distance (1000 m) buffer zones, with the maximal effects occurring in the 1000 m circular buffer (wet season) and 500 m riparian buffer (dry season) zone, respectively. Land use influenced the bacterioplankton community both directly through exogenous inputs (mass effect) and indirectly by affecting water chemistry (species sorting). Variance partitioning analyses showed that the total explanations of bacterial community variations by water chemistry and the intersections of water chemistry and land use (56.2% in wet season and 50.4% in dry season) were higher than that of land use alone (6.1% in wet season and 25.4% in dry season). These suggest that mass effects and species sorting jointly shaped bacterial community assembly, but that the effects of species sorting outweighed those of mass effects. Nevertheless, more biotic and abiotic factors need to be considered to better understand the microbial assembly mechanisms in anthropogenically influenced riverine ecosystems.

Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity

Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these "dynamic pulses of microbial life" for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.

Microbial communities in floodplain ecosystems in relation to altered flow regimes and experimental flooding

River floodplains are spatially diverse ecosystems that respond quickly to flow variations and disturbance. However, it remains unclear how flow alteration and hydrological disturbance impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we examined the spatial and seasonal dynamics of microbial communities in aquatic (benthic) and terrestrial habitats of three hydrologically contrasting (natural flow, residual flow, hydropeaking flow) floodplain systems. Microbial communities (alpha and beta diversity) differed more among floodplain habitats than between riverine floodplains. Microbial communities in all systems displayed congruent seasonal effects. In the residual and hydropeaking systems, an experimental flood was released from a reservoir to mimic a natural high flow event causing hydromorphological disturbance. The experimental flood caused a temporary shift in microbial communities by releasing microbes from the reservoir as well as redistributing communities among floodplain habitats. The flood-mediated shift in community structures had only a transient impact as pelagic bacteria did not persist within floodplain habitats over time after the flood. More frequent pulse disturbances might lead to an alternate structure of bacterial communities in floodplains over time.

Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data

Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.

Seasonal and spatial distribution and assembly processes of bacterioplankton communities in a subtropical urban river

The ecological functions of core and non-core bacteria are gradually being identified, yet little is known about their responses to environmental changes and assembly processes, especially in urban river ecosystems. Here, we investigated bacterioplankton communities over 1 year in an urban section of the Ganjiang River, China. The results revealed that the alpha- and beta-diversity of bacterioplankton communities had no significant spatial differences along the urbanization gradient, but they presented distinct seasonal variations. The bacterioplankton communities were comprised of a few core taxa (11.8%) and a large number of non-core taxa (88.2%), of which the non-core taxa were the most active component responsible for community dynamics. Most non-core taxa (76.84%) belonged to non-typical freshwater bacteria, implying that they are more likely to derive from allochthonous inputs than the core taxa. Variance partitioning analyses showed that air temperature, flow rate and water chemistry together explained 58.2 and 38.9% of the variations of the core taxa and non-core taxa, respectively. In addition, the relative importance of temperature and water chemistry on the bacterioplankton communities prevailed over that of flow rate alone. This means that deterministic processes and stochastic processes simultaneously control the bacterioplankton community assembly, with deterministic processes contributing more than stochastic processes.

Temporal variation in soil bacterial communities can be confounded with spatial variation

Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

Microbial community assembly in a multi-layer dendritic metacommunity

A major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks, branching patterns and directional flow can alter the balance between local and regional factors during assembly. Vertical habitat structure may further affect community assembly in dendritic metacommunities. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess differences in community assembly (1) between planktonic and benthic habitats, (2) across spatial scales, and (3) between headwater and downstream regions of the network. Using taxonomic and phylogenetic null modeling, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by variable selection, but we also found evidence of local dispersal limitation between the two habitats. Planktonic community assembly was scale dependent, transitioning from homogeneous selection at local scales to variable selection at regional scales, while benthic community assembly was less scale dependent. Variable selection structured headwaters in both habitat types, but downstream communities were primarily structured by homogeneous selection, especially in sediments. Taken together, our results show that vertical habitat structure contributes to the scale-dependent processes of community assembly across the dendritic metacommunity.

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake

Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.

Both microbial abundance and community composition mattered for N2 production rates of the overlying water in one high-elevation river

Overlying water is another potential hotspot of nitrogen removal through anammox and denitrification reactions in river systems. However, N₂ production and the controlling factors have rarely been investigated in the overlying water of high-elevation rivers. This study analyzed the abundance and community of denitrifying and anammox bacteria as well as their effects on N₂ production rates in the overlying water of the Yellow River source region (elevation range: 2687-4223 m). Higher suspended particle concentrations remarkably promoted functional gene abundances of both denitrifying and anammox bacteria (r > 0.9, p < 0.01). N₂ production rates in overlying water samples ranged from 0.25 to 4.22 μmol N₂ L^-1 d^-1. The overlying water was estimated to contribute to 36.8% (on average) of riverine N₂ emission flux. Higher temperatures markedly accelerated N₂ production rates (p = 0.051). Moreover, N₂ production rates were positively related to both anammox and denitrifying bacterial abundances (p < 0.05), and such relationships were markedly affected by corresponding community compositions. The explanatory power of denitrifier abundance (R² = 0.56) for N₂ production rate variations was greatly elevated when it was integrated with community composition (R² = 0.92). This study highlights the significance of overlying water nitrogen removal in the Yellow River source region; moreover, the effects of both microbial abundance and community composition on riverine N₂ production rates should be considered in future research.

Using soil bacterial communities to predict physico-chemical variables and soil quality

BACKGROUND

Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial community composition of over 3000 soil samples from 606 sites in New Zealand. Sites were classified as indigenous forests, exotic forest plantations, horticulture, or pastoral grasslands; soil physico-chemical variables related to soil quality were also collected. The composition of soil bacterial communities was then used to predict the land use and soil physico-chemical variables of each site.

RESULTS

Soil bacterial community composition was strongly linked to land use, to the extent where it could correctly determine the type of land use with 85% accuracy. Despite the inherent variation introduced by sampling across ~ 1300 km distance gradient, the bacterial communities could also be used to differentiate sites grouped by key physico-chemical properties with up to 83% accuracy. Further, individual soil variables such as soil pH, nutrient concentrations and bulk density could be predicted; the correlations between predicted and true values ranged from weak (R2 value = 0.35) to strong (R2 value = 0.79). These predictions were accurate enough to allow bacterial communities to assign the correct soil quality scores with 50-95% accuracy.

CONCLUSIONS

The inclusion of biological information when monitoring soil quality is crucial if we wish to gain a better, more accurate understanding of how land management impacts the soil ecosystem. We have shown that soil bacterial communities can provide biologically relevant insights on the impacts of land use on soil ecosystems. Furthermore, their ability to indicate changes in individual soil parameters shows that analysing bacterial DNA data can be used to screen soil quality. Video Abstract.

Method development for evaluating the effectiveness of hydrocarbons on BOD, UBOD and COD removal in oily wastewater

The effects of different operating parameters on the treatment efficiency of oily wastewater in terms of biological oxygen demand (BOD) and chemical oxygen demand (COD) were measured. The analyses of BOD using OxiTop biosensors are reviewed regarding performance characteristics like linearity, response time, precision, agreement between BOD₂₈ values obtained from the biosensors and the ultimate BOD (UBOD), as well as toxic resistance and COD. The wastewater samples were seeded with the bacteria, which were isolated in the current study from Kuwaiti oil-contaminated sand, such as Bacillus mycoidesis and Bacillus subtilis. After 18 days, the margin for saponin solution and oily wastewater using either Rhododcoccus (R), a mixture of Bacillus mycoidesis and Bacillus subtilis (M) or a mixture of R&M exhibited the maximum rate of BOD. It was found that the corresponding COD of the saponin solution (SS) ranged from 1,525 mg/l to 3,890 mg/l by distilled water and the mixture (RM), respectively. The COD of oily wastewater (WW) ranged from 2,900 mg/l to 4,450 mg/l by distilled water and the mixture of (RM), respectively. Moreover, the higher values of BOD₂₈ were recorded when mixtures of bacteria were added together with the saponin solution or oily wastewaters. Furthermore, the average values of UBOD for the oily wastewater with RM or with amendment substance were increased by about 33.5% and 49.5%, respectively. However, BOD ₂₈ /COD ratios for all the selected have been found to be less than 0.4, indicating low aerobic degradability.