Organic substrate quality as the link between bacterioplankton carbon demand and growth efficiency in a temperate salt-marsh estuary

Appropriate stoichiometric ratios of dissolved organic carbon and nitrate can trigger a transition in nitrate removal in groundwater around plateau lakes, Southwest China

Increasing dissolved organic carbon (DOC) in groundwater as a carbon source for microorganisms that stimulate nitrate attenuation is considered a sustainable strategy to mitigate nitrate pollution in groundwater. However, little is known on the stoichiometric ratio of DOC and nitrate required in groundwater nitrate reduction processes, which has become an obstacle for evaluating the current status of DOC limitations on nitrate reduction. Here, the NO3--N and DOC concentrations in groundwater around 8 plateau lakes were investigated, and a microcosm experiment was performed to elucidate the effects of different DOC:NO3--N levels in groundwater on NO3--N reduction, and the current status of DOC limitations on groundwater NO3--N reduction around 8 lakes was further evaluated. The results indicated that nearly 41 % of the groundwater NO3--N concentrations exceeded the WHO threshold for drinking water (11.3 mg L-1) and 79 % of the groundwater DOC concentrations exceeded 5 mg L-1. The differences in groundwater NO3--N and DOC concentrations among the 8 lakes were controlled by the intensity of agricultural and human activities and hydrogeological background. The stoichiometric ratio of DOC:NO3--N regulated the NO3--N reduction process, and groundwater NO3--N accumulation rate appeared to become limited and sharply decreased when the DOC concentration was approximately 10 mg L-1 or when the DOC:NO3--N ratio was close to 1:1, and the DOC:NO3--N ratio threshold for limiting the NO3--N reduction process was approximately 2.25. Based on this threshold, >33 %-86 % of the groundwater samples around the 8 plateau lakes were strongly limited in the reduction of groundwater NO3--N due to a lack of sufficient DOC provides energy for heterotrophic microorganisms. Additionally, we highlight that the sustainable strategy of increasing DOC to stimulate groundwater NO3- attenuation should be combined with short-term strategies to jointly coordinate and control groundwater NO3- pollution.

Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the 0.409-aw brine (an MgCl2-dominated site) despite the presence of cell-like structures. Extrapolating our data, we predict an aw limit for detectable anabolic activity of 0.540, which is beyond the currently accepted limit of life based on cell division. This work demonstrates the utility of single-cell, metabolism-based techniques for detecting active life and expands the potential habitable space on Earth and beyond.

Plastic pollution fosters more microbial growth in lakes than natural organic matter

Plastic debris widely pollutes freshwaters. Abiotic and biotic degradation of plastics releases carbon-based substrates that are available for heterotrophic growth, but little is known about how these novel organic compounds influence microbial metabolism. Here we found leachate from plastic shopping bags was chemically distinct and more bioavailable than natural organic matter from 29 Scandinavian lakes. Consequently, plastic leachate increased bacterial biomass acquisition by 2.29-times when added at an environmentally-relevant concentration to lake surface waters. These results were not solely attributable to the amount of dissolved organic carbon provided by the leachate. Bacterial growth was 1.72-times more efficient with plastic leachate because the added carbon was more accessible than natural organic matter. These effects varied with both the availability of alternate, especially labile, carbon sources and bacterial diversity. Together, our results suggest that plastic pollution may stimulate aquatic food webs and highlight where pollution mitigation strategies could be most effective.

Ultra-high resolution mass spectrometry revealed that plastic bags leach labile compounds. Bioassays performed in Scandinavian lakes indicated that these compounds are incorporated into biomass faster and more efficiently than natural organic matter.

The impact of eutrophication towards selected bacterial process rates in tropical coastal waters

The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R² ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.

Trait-based approach to bacterial growth efficiency

Bacterial growth efficiency (BGE) is the proportion of assimilated carbon that is converted into biomass and reflects the balance between growth and energetic demands. Often measured as an aggregate property of the community, BGE is highly variable within and across ecosystems. To understand this variation, we first identified how species identity and resource type affect BGE using 20 bacterial isolates belonging to the phylum Proteobacteria that were enriched from north temperate lakes. Using a trait-based approach that incorporated genomic and phenotypic information, we characterized the metabolism of each isolate and tested for predicted trade-offs between growth rate and efficiency. A substantial amount of variation in BGE could be explained at broad (i.e., order, 20%) and fine (i.e., strain, 58%) taxonomic levels. While resource type was a relatively weak predictor across species, it explained >60% of the variation in BGE within a given species. A metabolic trade-off (between maximum growth rate and efficiency) and genomic features revealed that BGE may be a species-specific metabolic property. Our study suggests that genomic and phylogenetic information may help predict aggregate microbial community functions like BGE and the fate of carbon in ecosystems.

Exoenzymes as a Signature of Microbial Response to Marine Environmental Conditions

Microbial heterotopic metabolism in the ocean is fueled by a supply of essential nutrients acquired via exoenzymes catalyzing depolymerization of high-molecular-weight compounds. Although the rates of activity for a variety of exoenzymes across various marine environments are well established, the factors regulating the production of these exoenzymes, and to some extent their correlation with microbial community composition, are less known. This study focuses on addressing these challenges using a mesocosm experiment that compared a natural seawater microbial community (control) and exposed (to oil) treatment. Exoenzyme activities for β-glucosidase, leucine aminopeptidase (LAP), and lipase were significantly correlated with dissolved nutrient concentrations. We measured correlations between carbon- and nitrogen-acquiring enzymes (β-glucosidase/lipase versus LAP) and found that the correlation of carbon-acquiring enzymes varies with the chemical nature of the available primary carbon source. Notably, a strong correlation between particulate organic carbon and β-glucosidase activity demonstrates their polysaccharide depolymerization in providing the carbon for microbial growth. Last, we show that exoenzyme activity patterns are not necessarily correlated with prokaryotic community composition, suggesting a redundancy of exoenzyme functions among the marine microbial community and substrate availability. This study provides foundational work for linking exoenzyme function with dissolved organic substrate and downstream processes in marine systems.IMPORTANCE Microbes release exoenzymes into the environment to break down complex organic matter and nutrients into simpler forms that can be assimilated and utilized, thereby addressing their cellular carbon, nitrogen, and phosphorus requirements. Despite its importance, the factors associated with the synthesis of exoenzymes are not clearly defined, especially for the marine environment. Here, we found that exoenzymes associated with nitrogen and phosphorus acquisition were strongly correlated with inorganic nutrient levels, while those associated with carbon acquisition depended on the type of organic carbon available. We also show a linear relationship between carbon- and nitrogen-acquiring exoenzymes and a strong correlation between microbial biomass and exoenzymes, highlighting their significance to microbial productivity. Last, we show that changes in microbial community composition are not strongly associated with changes in exoenzyme activity profiles, a finding which reveals a redundancy of exoenzyme activity functions among microbial community. These findings advance our understanding of previously unknown factors associated with exoenzyme production in the marine environment.

Dissolved Organic Carbon Source Influences Tropical Coastal Heterotrophic Bacterioplankton Response to Experimental Warming

Global change impacts on marine biogeochemistry will be partly mediated by heterotrophic bacteria. Besides ocean warming, future environmental changes have been suggested to affect the quantity and quality of organic matter available for bacterial growth. However, it is yet to be determined in what way warming and changing substrate conditions will impact marine heterotrophic bacteria activity. Using short-term (4 days) experiments conducted at three temperatures (−3°C, in situ, +3°C) we assessed the temperature dependence of bacterial cycling of marine surface water used as a control and three different dissolved organic carbon (DOC) substrates (glucose, seagrass, and mangrove) in tropical coastal waters of the Great Barrier Reef, Australia. Our study shows that DOC source had the largest effect on the measured bacterial response, but this response was amplified by increasing temperature. We specifically demonstrate that (1) extracellular enzymatic activity and DOC consumption increased with warming, (2) this enhanced DOC consumption did not result in increased biomass production, since the increases in respiration were larger than for bacterial growth with warming, and (3) different DOC bioavailability affected the magnitude of the microbial community response to warming. We suggest that in coastal tropical waters, the magnitude of heterotrophic bacterial productivity and enzyme activity response to warming will depend partly on the DOC source bioavailability.

Recurrent seasonal changes in bacterial growth efficiency, metabolism and community composition in coastal waters

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (T_A ) and September (T_S ). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before T_A and the bloom of prokaryotic phytoplankton before T_S . Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.

Response of Bacterial Metabolic Activity to the River Discharge in the Pearl River Estuary: Implication for CO2 Degassing Fluxes

Bacterial production (BP), respiration (BR) and growth efficiency (BGE) were simultaneously determined along an environmental gradient in the Pearl River Estuary (PRE) in the wet season (May 2015) and the dry season (January 2016), in order to examine bacterial responses to the riverine dissolved organic carbon (DOC) in the PRE. The Pearl River discharge delivered labile dissolved organic matters (DOM) with low DOC:DON ratio, resulting in a clear gradient in DOC concentrations and DOC:DON ratios. BP (3.93-144 μg C L^-1 d^-1) was more variable than BR (64.6-567 μg C L^-1 d^-1) in terms of the percentage, along an environmental gradient in the PRE. In response to riverine DOC input, BP and the cell-specific BP increased; in contrast, the cell-specific bacterial respiration declined, likely because labile riverine DOC mitigated energetic cost for cell maintenance. Consequently, an increase in bacterial respiration was less than expected. Our findings implied that the input of highly bioavailable riverine DOC altered the carbon portioning between anabolic and catabolic pathways, consequently decreasing the fraction of DOC that bacterioplankton utilized for bacterial respiration. This might be one of the underlying mechanisms for the low CO₂ degassing in the PRE receiving large amounts of sewage DOC.

Photochemical alteration of dissolved organic matter and the subsequent effects on bacterial carbon cycling and diversity

The impact of solar radiation on dissolved organic matter (DOM) derived from 3 different sources (seawater, eelgrass leaves and river water) and the effect on the bacterial carbon cycling and diversity were investigated. Seawater with DOM from the sources was first either kept in the dark or exposed to sunlight (4 days), after which a bacterial inoculum was added and incubated for 4 additional days. Sunlight exposure reduced the coloured DOM and carbon signals, which was followed by a production of inorganic nutrients. Bacterial carbon cycling was higher in the dark compared with the light treatment in seawater and river samples, while higher levels were found in the sunlight-exposed eelgrass experiment. Sunlight pre-exposure stimulated the bacterial growth efficiency in the seawater experiments, while no impact was found in the other experiments. We suggest that these responses are connected to differences in substrate composition and the production of free radicals. The bacterial community that developed in the dark and sunlight pre-treated samples differed in the seawater and river experiments. Our findings suggest that impact of sunlight exposure on the bacterial carbon transfer and diversity depends on the DOM source and on the sunlight-induced production of inorganic nutrients.

Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system

This study explores the role of transparent exopolymer particles (TEP) as an additional carbon source for heterotrophic microbial activity in the eutrophic Qishon estuary. From the coastal station and upstream the estuary; TEP concentrations, β-glucosidase activity, bacterial production and abundance have gradually increased. TEP were often found as bio-aggregates, scaffolding algae, detritus matter and bacteria that likely formed “hotspots” for enhance microbial activity. To further demonstrate the link between TEP and heterotrophic bacterial activity, confined incubations with ambient and polysaccharide-enriched estuary water were carried out. Following polysaccharide addition, elevated (~50%) β-glucosidase activity rates were observed, leading to TEP hydrolysis. This newly formed bioavailable carbon resulted in significantly higher growth rates, with up to a 5-fold increase in heterotrophic bacterial biomass, comprising mostly high nucleic acid content bacteria. Taking together the findings from this research, we conclude that even in highly eutrophic environments heterotrophic bacteria may still be carbon limited. Further, TEP as a polysaccharide matrix can act as a metabolic surrogate, adding fresh bioavailable carbon through tight associations with bacteria in eutrophic ecosystems such as the Qishon estuary.

Stoichiometric determination of nitrate fate in agricultural ecosystems during rainfall events

Ecologists have found a close relationship between the concentrations of nitrate (NO3-) and dissolved organic carbon (DOC) in ecosystems. However, it is difficult to determine the NO3- fate exactly because of the low coefficient in the constructed relationship. In the present paper, a negative power-function equation (r(2) = 0.87) was developed by using 411 NO3- data points and DOC:NO3- ratios from several agricultural ecosystems during different rainfall events. Our analysis of the stoichiometric method reveals several observations. First, the NO3- concentration demonstrated the largest changes when the DOC:NO3- ratio increased from 1 to 10. Second, the biodegradability of DOC was an important factor in controlling the NO3- concentration of agricultural ecosystems. Third, sediment was important not only as a denitrification site, but also as a major source of DOC for the overlying water. Fourth, a high DOC concentration was able to maintain a low NO3- concentration in the groundwater. In conclusion, this new stoichiometric method can be used for the accurate estimation and analysis of NO3- concentrations in ecosystems.

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Photochemical and microbial alterations of DOM spectroscopic properties in the estuarine system Ria de Aveiro

The chromophoric dissolved organic matter (CDOM) of marine (MZ) and brackish water (BZ) zones of Ria de Aveiro showed different spectral characteristics and susceptibility to photochemical alterations, reflecting the different amounts and prevailing sources of organic matter.

Thermal adaptation of decomposer communities in warming soils

Temperature regulates the rate of biogeochemical cycles. One way it does so is through control of microbial metabolism. Warming effects on metabolism change with time as physiology adjusts to the new temperature. I here propose that such thermal adaptation is observed in soil microbial respiration and growth, as the result of universal evolutionary trade-offs between the structure and function of both enzymes and membranes. I review the basis for these trade-offs and show that they, like substrate depletion, are plausible mechanisms explaining soil respiration responses to warming. I argue that controversies over whether soil microbes adapt to warming stem from disregarding the evolutionary physiology of cellular metabolism, and confusion arising from the term thermal acclimation to represent phenomena at the organism- and ecosystem-levels with different underlying mechanisms. Measurable physiological adjustments of the soil microbial biomass reflect shifts from colder- to warmer-adapted taxa. Hypothesized declines in the growth efficiency of soil microbial biomass under warming are controversial given limited data and a weak theoretical basis. I suggest that energy spilling (aka waste metabolism) is a more plausible mechanism for efficiency declines than the commonly invoked increase in maintenance-energy demands. Energy spilling has many fitness benefits for microbes and its response to climate warming is uncertain. Modeled responses of soil carbon to warming are sensitive to microbial growth efficiency, but declines in efficiency mitigate warming-induced carbon losses in microbial models and exacerbate them in conventional models. Both modeling structures assume that microbes regulate soil carbon turnover, highlighting the need for a third structure where microbes are not regulators. I conclude that microbial physiology must be considered if we are to have confidence in projected feedbacks between soil carbon stocks, atmospheric CO₂, and climate change.

Phosphorus and DOC availability influence the partitioning between bacterioplankton production and respiration in tidal marsh ecosystems

The organic carbon consumed by aquatic bacteria (BCC) is partitioned between bacterial production (BP) and respiration (BR), but the factors that determine BCC and its partition into BP and BR are not well understood. We explored the coupling between BR, BR and BCC, and their links to dissolved organic carbon (DOC) and nutrient availability in natural and restored tidal marshes and in the adjoining waters of Delaware Bay estuary. Labile DOC (LDOC) ranged from 3% to 22% of the DOC pool, and explained more of the variance in both BR and BCC than did bulk DOC. Bacterial growth efficiency (BGE) was highly variable (0.09-0.58), and natural Spartina alterniflora marshes had consistently higher BGE than both restoration marshes and tidal floodwaters. BGE was negatively related to the ratio of LDOC to total dissolved phosphorous, which was highest in natural marshes. The enhancement of BP observed in the marshes relative to the estuarine floodwaters had different origins: In natural marshes it was mostly due to increases in BGE, whereas in restored marshes it followed increased BCC. These results highlight the importance of P in regulating microbial metabolism in coastal areas, and the need to understand the pathways that lead to BP in these systems.

Stoichiometric control of organic carbon-nitrate relationships from soils to the sea

The production of artificial fertilizers, fossil fuel use and leguminous agriculture worldwide has increased the amount of reactive nitrogen in the natural environment by an order of magnitude since the Industrial Revolution. This reorganization of the nitrogen cycle has led to an increase in food production, but increasingly causes a number of environmental problems. One such problem is the accumulation of nitrate in both freshwater and coastal marine ecosystems. Here we establish that ecosystem nitrate accrual exhibits consistent and negative nonlinear correlations with organic carbon availability along a hydrologic continuum from soils, through freshwater systems and coastal margins, to the open ocean. The trend also prevails in ecosystems subject to substantial human alteration. Across this diversity of environments, we find evidence that resource stoichiometry (organic carbon:nitrate) strongly influences nitrate accumulation by regulating a suite of microbial processes that couple dissolved organic carbon and nitrate cycling. With the help of a meta-analysis we show that heterotrophic microbes maintain low nitrate concentrations when organic carbon:nitrate ratios match the stoichiometric demands of microbial anabolism. When resource ratios drop below the minimum carbon:nitrogen ratio of microbial biomass, however, the onset of carbon limitation appears to drive rapid nitrate accrual, which may then be further enhanced by nitrification. At low organic carbon:nitrate ratios, denitrification appears to constrain the extent of nitrate accretion, once organic carbon and nitrate availability approach the 1:1 stoichiometry of this catabolic process. Collectively, these microbial processes express themselves on local to global scales by restricting the threshold ratios underlying nitrate accrual to a constrained stoichiometric window. Our findings indicate that ecological stoichiometry can help explain the fate of nitrate across disparate environments and in the face of human disturbance.

Temporal variation of bacterial respiration and growth efficiency in tropical coastal waters

We investigated the temporal variation of bacterial production, respiration, and growth efficiency in the tropical coastal waters of Peninsular Malaysia. We selected five stations including two estuaries and three coastal water stations. The temperature was relatively stable (averaging around 29.5 degrees C), whereas salinity was more variable in the estuaries. We also measured dissolved organic carbon and nitrogen (DOC and DON, respectively) concentrations. DOC generally ranged from 100 to 900 microM, whereas DON ranged from 0 to 32 microM. Bacterial respiration ranged from 0.5 to 3.2 microM O2 h(-1), whereas bacterial production ranged from 0.05 to 0.51 microM C h(-1). Bacterial growth efficiency was calculated as bacterial production/(bacterial production + respiration), and ranged from 0.02 to 0.40. Multiple correlation analyses revealed that bacterial production was dependent upon primary production (r2 = 0.169, df = 31, and P < 0.02) whereas bacterial respiration was dependent upon both substrate quality (i.e., DOC/DON ratio) (r2 = 0.137, df = 32, and P = 0.03) and temperature (r2 = 0.113, df = 36, and P = 0.04). Substrate quality was the most important factor (r2 = 0.119, df = 33, and P = 0.04) for the regulation of bacterial growth efficiency. Using bacterial growth efficiency values, the average bacterial carbon demand calculated was from 5.30 to 11.28 microM C h(-1). When the bacterial carbon demand was compared with primary productivity, we found that net heterotrophy was established at only two stations. The ratio of bacterial carbon demand to net primary production correlated significantly with bacterial growth efficiency (r2 = 0.341, df = 35, and P < 0.001). From nonlinear regression analysis, we found that net heterotrophy was established when bacterial growth efficiency was <0.08. Our study showed the extent of net heterotrophy in these waters and illustrated the importance of heterotrophic microbial processes in coastal aquatic food webs.