Heterotrophic Microbial Communities Research Articles

Metabolite release by nitrifiers facilitates metabolic interactions in the ocean.

Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.

Environmental control and metabolic strategies of organic-matter-responsive bacterioplankton in the Weddell Sea (Antarctica).

Heterotrophic microbial communities play a significant role in driving carbon fluxes in marine ecosystems. Despite their importance, these communities remain understudied in remote polar oceans, which are known for their substantial contribution to the biological drawdown of atmospheric carbon dioxide. Our research focused on understanding the environmental factors and genetic makeup of key bacterial players involved in carbon remineralization in the Weddell Sea, including its coastal polynyas. Our experiments demonstrated that the combination of labile organic matter supply and temperature increase synergistically boosted bacterial growth. This suggests that, besides low seawater temperature, carbon limitation also hinders heterotrophic bacterial activity. Through the analysis of metagenome-assembled genomes, we discovered distinct genomic adaptation strategies in Bacteroidia and Gammaproteobacteria, both of which respond to organic matter. Both natural phytoplankton blooms and experimental addition of organic matter favoured Bacteroidia, which possess a large number of gene copies and a wide range of functional membrane transporters, glycoside hydrolases, and aminopeptidases. In contrast, the genomes of organic-matter-responsive Gammaproteobacteria were characterized by high densities of transcriptional regulators and transporters. Our findings suggest that bacterioplankton in the Weddell Sea, which respond to organic matter, employ metabolic strategies similar to those of their counterparts in temperate oceans. These strategies enable efficient growth at extremely low seawater temperatures, provided that organic carbon limitation is alleviated.

Mechanisms Underpinning the Net Removal Rates of Dissolved Organic Carbon in the Global Ocean

AbstractWith almost 700 Pg of carbon, marine dissolved organic carbon (DOC) stores more carbon than all living biomass on Earth combined. However, the controls behind the persistence and the spatial patterns of DOC concentrations on the basin scale remain largely unknown, precluding quantitative assessments of the fate of this large carbon pool in a changing climate. Net removal rates of DOC along the overturning circulation suggest lifetimes of millennia. These net removal rates are in stark contrast to the turnover times of days to weeks of heterotrophic microorganisms, which are the main consumers of organic carbon in the ocean. Here, we present a dynamic “MICrobial DOC” model (MICDOC) with an explicit representation of picoheterotrophs to test whether ecological mechanisms may lead to observed decadal to millennial net removal rates. MICDOC is in line with >40,000 DOC observations. Contrary to other global models, the reactivity of DOC fractions is not prescribed, but emerges from a dynamic feedback between microbes and DOC governed by carbon and macronutrient availability. A colimitation of macronutrients and organic carbon on microbial DOC uptake explains >70% of the global variation of DOC concentrations, and governs characteristic features of its distribution. Here, decadal to millennial net removal rates emerge from microbial processes acting on time scales of days to weeks, suggesting that the temporal variability of the marine DOC inventory may be larger than previously thought. With MICDOC, we provide a foundation for assessing global effects on DOC related to changes in heterotrophic microbial communities in a future ocean.

The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions.

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

Assessment of functional diversity of heterotrophic microbial communities in polluted environments through community level physiological profiles

The community level physiological profiles (CLPP) of bacterial communities inhabiting polluted environments (acid mine drainage water and sediments, soils contaminated with tannery waste and oil refinery effluents) were assessed using the Biolog Ecoplates™ in comparison to non-contaminated sites (water and sediments from a recreational lake and soil from anopen space). Although the polluted sites were characterized by typically high metal concentrations, CLPP fingerprints of the different bacterial communities from these sites were indicative of versatile metabolic potentials. These microbial communities could differentially utilize all the different groups of carbon substrates. However, the rates of utilization were significantly lower, and the number of utilized substrates were fewer than those of microbial communities from non-contaminated sites. This was confirmed by cluster analysis in which the dendrogram showed two clusters of microbial communities from contaminated environments and another for those from non-contaminated sites. Nonetheless, the indices of diversity calculated did not show a reduction of diversity or evenness in the microbial communities from contaminated sites. This study confirms the usefulness of the CCLP method in untangling the functional diversity of microbial diversity in contaminated environments.

Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen.

Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.

Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.

Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.

Differences Between Heterotrophic and Nitrate-dependent Iron-oxidizing Microbial Communities in Bioreactor Sediment Treating Mine Wastewater

Nitrate-dependent iron oxidation (NDFO) is a novel mechanism for microbial bioremediation of metal and metalloid contaminants. During NDFO, microbes catalyze a redox reaction wherein nitrate is reduced to nitrite and nitrogen gas while Fe(II) is oxidized to solid Fe(III) hydroxide minerals. Metalloid contaminants such as selenium and arsenic have a propensity for adsorption to iron minerals produced during NDFO; some contaminants may also be concurrently bioreduced. A number of bacterial isolates have been shown to be capable of NDFO (e.g., Kappler et al. (2005), Kiskira et al. (2017)), but little work has been done to date characterizing mixed microbial communities performing NDFO. Some autotrophic communities have been characterized, with high relative abundances for strains of Gallionellaceae in both a freshwater sediment enrichment culture and an activated sludge culture (Blöthe and Roden 2009, Tian et al. 2020). In mixotrophic activated sludge cultures, the concentration of Fe(II) amendment was found to significantly impact microbial community composition; these cultures were fed with methanol in addition to Fe(II), and the dominant community members were Methyloversatilis and other methylotrophic strains (Liu et al. 2018). The work presented here examines microbial communities performing NDFO in the context of remediation, and in particular how differences between NDFO and heterotrophic communities may influence remediation effectiveness. This research characterizes and compares microbial communities performing NDFO versus heterotrophic denitrification during removal of selenium and nickel from mining wastewater. Sediment and influent water from a subsurface bioreactor treating mining wastewater were used to construct batch bioreactors, which were amended with selenium and nickel as well as either Fe(II) or methanol to investigate contaminant removal and microbial community composition in NDFO versus heterotrophic microbial communities. Both Fe(II) and methanol reactors removed total aqueous selenium to below the quantification limit, but Fe(II) reactors removed it more rapidly, likely due to adsorption of selenite. For nickel, removal to below the detection limit was achieved with methanol amendment, while Fe(II) amendment resulted in 42-95% removal. This was likely due to precipitation of nickel sulfide during sulfate reduction in methanol-amended reactors. DNA from the batch bioreactors will be sequenced and the results analyzed for differences among communities. Permutational multivariate analysis of variance and non-metric multidimensional scaling will be used to determine significant correlations of community composition with experimental variables, selenium and nickel removal, and NDFO (Roberts 2023, Kruskal 1964). Indicator species analyses (De Cáceres et al. 2010) will be applied to identify taxa found significantly more often (i.e., at a higher relative abundance) in one group of microbial communities than in any other group. The indicator species analysis may reveal whether there are groups of denitrifiers that predominate in NDFO conditions vs. groups that predominate during heterotrophic denitrification. The results of these microbial community analyses, in combination with the geochemical analyses, will improve our understanding of microbial communities performing NDFO in remediation environments.

Identification of microbial metabolic functional guilds from large genomic datasets.

Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, the consumption rate of organic matter is set by the interaction between diverse microbial communities and the chemical and physical environment in which they reside. Modeling these dynamics requires reducing the complexity of microbial communities and linking directly with biogeochemical functions. Microbial metabolic functional guilds provide one approach for reducing microbial complexity and incorporating microbial biogeochemical functions into models. However, we lack a way to identify these guilds. In this study, we present a method for defining metabolic functional guilds from annotated genomes, which are derived from both uncultured and cultured organisms. This method utilizes an Aspect Bernoulli (AB) model and was tested on three large genomic datasets with 1,733-3,840 genomes each. Ecologically relevant microbial metabolic functional guilds were identified including guilds related to DMSP degradation, dissimilatory nitrate reduction to ammonia, and motile copiotrophy. This method presents a way to generate hypotheses about functions co-occurring within individual microbes without relying on cultured representatives. Applying the concept of metabolic functional guilds to environmental samples will provide new insight into the role that heterotrophic microbial communities play in setting rates of carbon cycling.

Responses to organic pollutants in the tropical Pacific and subtropical Atlantic Oceans by pelagic marine bacteria

Background and chronic pollution by organic pollutants (OPs) is a widespread threat in the oceans with still uncharacterized effects on marine ecosystems and the modulation of major biogeochemical cycles. The ecological impact and toxicity of this anthropogenic dissolved organic carbon (ADOC) is not related to the presence of a single compound but to the co-occurrence of a myriad of synthetic chemicals with largely unknown effects on heterotrophic microbial communities. We have analyzed the metabolic capacity of metagenome-assembled genomes (MAGs) of natural oceanic communities from the north Pacific (Costa Rica dome) and Atlantic oceans challenged with environmentally relevant levels of ADOC. In the Atlantic, ADOC-exposed MAGs responded transcriptionally more strongly compared to controls than in the Pacific, possibly mirroring the higher relevance of ADOC compounds as carbon source in oligotrophic environments. The largest proportions of transcripts originated from MAGs belonging in the families Rhodobacteraceae and Flavobacteriaceae, known to play a role on consumption of several OPs. In the Atlantic, archaeal Poseidoniales showed the highest transcription levels after 2 h of ADOC exposure, although no increase of relative abundances in the DNA pool was recorded after 24 h, whereas Methylophaga showed the opposite pattern. Both taxa are suggested to be actively involved in the consumption of biogenic alkanes produced by cyanobacteria. We observed similar gene expression profiles of alkane degradation and methylotrophy signature genes. These findings, plus the chemical degradation of alkanes measured in the experiments, provides experimental evidence of the consumption of anthropogenic hydrocarbons and synthetic chemicals at the low concentrations found in the ocean, and modulation of microbiomes by ADOC.

Terrigenous particles regulate autotrophic and heterotrophic microbial assembly and induce humic-like FDOM accumulation in seawater

Climate change can increase riverine discharge, which will promote terrigenous particle transportation and deeply impact microbe-mediated biogeochemical processes in the estuarine ecosystem. However, little is known about the long-term impacts of terrigenous particles on autotrophic and heterotrophic microbial community structures due to in situ continuous particle input. To solve this problem, a large-volume indoor incubation experiment was set up for over 40 days to simulate terrigenous particle input scenario. The activity and community structures of keystone groups were largely correlated with biochemical components derived from the terrigenous particles. The ecosystem was maintained by chemoautotrophic nitrifiers before the addition of terrigenous particles. The system was then functionally dominated by heterotrophic microorganisms after the input of terrigenous particles because terrigenous particles created environments that allowed heterotrophs to proliferate better than chemoautotrophs. The input of terrigenous particles increased the relative intensity of humic-like compounds mainly through releasing nutrients and biological labile organic matter to the seawater, which promoted the microbial transformation of organic matter. This study illustrates that terrigenous particles can impact the balance between heterotrophic and chemoautotrophic microbes and play an important role in humic-like compound transformation in seawater.

Biofloc colors as an assessment tool for water quality in shrimp farming with BFT systems

In shrimp farming using biofloc technology it is common to observe a gradual swap in the biofloc colors from green to brown along with shifts in water quality throughout the culture cycle. This change reflects a dominance shift from an autotrophic to a heterotrophic microbial community, resulting mainly from changes in system C:N and N:P ratios. Notwithstanding the ease of the direct analysis of biofloc color, no assessment of its potential as a proxy of water quality has been done so far. Therefore, our aim was to develop a standardized protocol to determine the potential of using the microbial community color index (MCCI) to develop an easy, fast, and low-cost assessment of water quality of intensive marine shrimp farming using biofloc systems. In this study, water quality data were collected from 17 tanks and the biofloc color was obtained from images after filtering with the help of an apparatus built with materials accessible to shrimp producers. We developed and standardized a methodology for reading the average RGB (Red, Green, and Blue) values from pixels of bioflocs images and used this methodology to calculate their average MCCIs. Based on this quantification of colors, it was possible to calculate a correlation matrix among MCCI and several water quality variables. The MCCI was positively correlated with the concentration of carbon, nitrogen, and phosphorus concentration in the bioflocs, total suspended solids, settleable solids and total phosphorus and negatively correlated with water transparency and G (green) values. The MCCI association with important water quality variables was expected for this type of system, in which the dominance by heterotrophic bacteria occurs at the final stages of biofloc succession, during which the system undergoes nutrient accumulation, shifting the bioflocs color from green to brown shades. Thus, it was observed that the water quality variables correlated with the MCCI were those that varied according to the culture stage. Another important result was that artificial images generated from images’ average RGB yielded satisfactory results regarding the similarity to the original images. Therefore, since it is possible to estimate water quality variables from the biofloc colors, this method lays the foundation for the future development of a practical tool (color scale or mobile app) for water quality evaluation. Shrimp farmers can use it to conduct a cheap and fast assessment of water quality of their tanks and take better decisions about critical aspects such as fertilization, water renewal or mechanical removal of excessive concentration of bioflocs.

New insights into the patterns of ecoenzymatic stoichiometry in soil and sediment

Ecoenzymatic stoichiometry connects the elemental stoichiometry of microbial biomass and detrital organic matter to microbial nutrient assimilation and growth, and thus has been proposed and developed to estimate microbial nutrient limitations. However, the theories and methods developed so far have not yet clearly explored the critical thresholds of ecoenzymatic stoichiometry that identify whether nutrient limitation occurs or not. Here, we developed methods quantifying critical thresholds for microbial carbon (C), nitrogen (N) and phosphorus (P) limitations by centering on the potential responses of microbial resource use efficiency to nutrient limitations. We also provided new insight into the relationships of bivariate regressions between C-, N- and P-acquiring ecoenzymatic activities by reconsidering the intercept of regressions as an index to initial nutrient limitations, and consequently distinguished six initial limitation scenarios based on the range of values for these intercepts. According to the empirical values of the regression intercepts, the overall frequency of primary nutrient limitations in microbial communities across a global suite of soils and sediments is P limitation > N limitation > C limitation. The result implies that P and N availabilities rather than that of C could be the most important limitations on microbial production and metabolism in terrestrial soils and freshwater sediments. Nutrient limitations in heterotrophic microbial communities are fundamental characteristics of both soil and sediment systems, which regulate organic matter decomposition and element cycles. Our perspective provides a foundational framework and avenue for understanding and quantifying microbial nutrient limitations in studies of terrestrial C cycling and microbial ecology.

Studying the state of the habitat of water biological resources of the Northern Caspian on microbiological indicators

In the spring of 2020, in most of the water area of the northern Caspian, the prevalence of saprotrophic floras did not exceed 50000 cells/ml, which microbiota level in summer. The number of oligotrophs in most of the water area was inferior to saprotrophs, which indicated an mbalance in the heterotrophic microbial community. In summer, in the northern part of the Caspian Sea, a decrease in the average heterotrophic group of bacterioplankton and bacteriobenthos was recorded, which indicated the process of self-purification of the marine environment from allochthonous elements. Viewing in the summer period in the waters of the Northern Caspian Sea, the zone of the zone with water saprobicity corresponding to the “polluted” category, the process of self-cleaning of the reservoir after the spring flood was not completed. In the autumn of 2020, the distribution of heterotrophic bacterioplankton and bacteriobenthos reached its lowest levels for all periods of research. In water, the number of saprotrophs was inferior to oligotrophs, which indicated the presence of a heterotrophic microbiota in the water, but they remained in the zone of increased saprobicity. An analysis of the taxonomic structure microbiota showed that heterotrophic communities of bacterioplankton and bacteriobenthos form representatives of the 6th family of gram-negative bacteria (Alsaligenaceae,Enterobacteriaceae, Flavobacteriaceae, Moraxellaceae, Pseudomonadaceae and Vibrionaceae), as well as gram-positive microorganisms. Gram-positive bacteria are most often found in enrichment cultures, mainly of the listed families. Some of the isolated bacteria belong to the group of opportunistic pathogens, which led to the identification of a potential danger to aquatic organisms. However, most of the identified representatives are true saprophytes, covering the inhabitants of water and bottom sediments. The predominance of indigenous microbiocenosis tends to reduce the bacterial pressure of the ecosystem in the water area and improve the state of the habitat of aquatic biological resources in terms of biological micro-characteristics.

Microbial Extracellular Enzymatic Activity Unveils the Anthropic Impact on Riparian Ecosystems From Southern Romania

The anthropization processes can cause complex, often irreversible changes in natural ecosystems. Several decades ago, on the upper course of the Arges River flowing in the Southern Romania, a series of anthropic interventions took place, which resulted in several new accumulation lakes. Above the socioeconomic benefit to the local communities along the watercourse, their construction also influenced the structure and functioning of the existing ecosystems. In the present study, we have analysed the rate of the detrital organic matter decomposition processes achieved by the heterotrophic microbial communities in several ecosystems located on the upper course of the river. The obtained results revealed that the intensity of these procceses was infleunced both by the type of anthropic area the sampled ecosystems attain - rural or urban, and by the sampling time.

Historical contingencies and phage induction diversify bacterioplankton communities at the microscale

In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse of populations on these resource patches unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of heterotrophic metabolism. Despite the potential importance of patch-level dynamics for the large-scale functioning of heterotrophic microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we address this challenge by characterizing the natural marine communities that assembled on over 1,000 individual microscale particles of chitin, the most abundant marine polysaccharide. Using low-template shotgun metagenomics and imaging, we find significant variation in microscale community composition despite the similarity in initial species pools across replicates. Chitin-degrading taxa that were rare in seawater established large populations on a subset of particles, resulting in a wide range of predicted chitinolytic abilities and biomass at the level of individual particles. We show, through a mathematical model, that this variability can be attributed to stochastic colonization and historical contingencies affecting the tempo of growth on particles. We find evidence that one biological process leading to such noisy growth across particles is differential predation by temperate bacteriophages of chitin-degrading strains, the keystone members of the community. Thus, initial stochasticity in assembly states on individual particles, amplified through ecological interactions, may have significant consequences for the diversity and functionality of systems of microscale patches.

Response of Heterotrophic Microbial Communities to an Environmental Gradient in the Floodplain of Mapire River, Venezuela

Soil physico-chemical characteristics of floodplains, particularly hydrology, influence microbiological activity. As such, each river floodplain system has a unique physico-chemical dynamic that in turn supports the microbial community. The Mapire River floodplain is a complex system in which seasonal flood pulses cause changes in the soil physico-chemical variables. We examined how these temporal and spatial differences are associated with the microbiological activity along a seasonally flooded gradient at the mouth of the Mapire River (Lower Orinoco, Venezuela). Soil samples were collected during three different seasons by a systematic sampling at 4 points of the gradient, defined by the intensity of flooding. The physico-chemical parameters of the soil were determined and related by the density and physiological profile of the microbial community through multivariate permutation analysis and gradient analysis. The results indicate that there is a spatial gradient determined by soil clay content and a temporal gradient influenced by moisture and total organic carbon. Significant differences were found among soil zones and seasons, with the interaction of both factors also significant. It was observed that microbial activity is decisive in phosphorus dynamics, even during flooding. It is concluded that amid the complex interactions between biotic and abiotic factors, microbial communities are able to respond to changes in the physico-chemical soil environment and maintain their activity throughout the hydroperiod.

Hydrolysis of Methylumbeliferyl Substrate Proxies for Esterase Activities as Indicator for Microbial Oil Degradation in the Ocean: Evidence from Observations in the Aftermath of the Deepwater Horizon Oil Spill (Gulf of Mexico)

Biological oil weathering facilitated by specialized heterotrophic microbial communities plays a key role in the fate of petroleum hydrocarbon in the ocean. The most common methods of assessing oil biodegradation involve (i) measuring changes in the composition and concentration of oil over time and/or (ii) biological incubations with stable or radio-labelled substrates. Both methods provide robust and invaluable information on hydrocarbon biodegradation pathways; however, they also require extensive sample processing and are expensive in nature. More convenient ways to assess activities within microbial oil degradation networks involve measuring extracellular enzyme activity. This perspective article synthesizes previously published results from studies conducted in the aftermath of the 2010 Deepwater Horizon (DwH) oil spill in the northern Gulf of Mexico (nGoM), to test the hypothesis that fluorescence assays of esterases, including lipase activity, are sensitive indicators for microbial oil degradation in the ocean. In agreement with the rates and patterns of enzyme activity in oil-contaminated seawater and sediments in the nGoM, we found close correlations between esterase activity measured by means of methylumbeliferyl (MUF) oleate and MUF butyrate hydrolysis, and the concentration of petroleum hydrocarbons in two separate laboratory incubations using surface (<1 m) and deep nGoM waters (>1200 m). Correlations between esterase activities and oil were driven by the presence of chemical dispersants, suggesting a connection to the degree of oil dissolution in the medium. Our results clearly show that esterase activities measured with fluorogenic substrate proxies are a good indicator for oil biodegradation in the ocean; however, there are certain factors as discussed in this study that need to be taken into consideration while utilizing this approach.

Metabolic cross-feeding structures the assembly of polysaccharide degrading communities.

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders structure the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical cross-feeding structure that allows biopolymer degraders to shape the dynamics of community assembly.

Quorum Sensing Regulates the Hydrolytic Enzyme Production and Community Composition of Heterotrophic Bacteria in Coastal Waters.

Heterotrophic microbial communities play a central role in biogeochemical cycles in the ocean by degrading organic matter through the synthesis of extracellular hydrolytic enzymes. Their hydrolysis rates result from the community’s genomic potential and the differential expression of this genomic potential. Cell-cell communication pathways such as quorum sensing (QS) could impact both aspects and, consequently, structure marine ecosystem functioning. However, the role of QS communications in complex natural assemblages remains largely unknown. In this study, we investigated whether N-acylhomoserine lactones (AHLs), a type of QS signal, could regulate both hydrolytic activities and the bacterial community composition (BCC) of marine planktonic assemblages. To this extent, we carried out two microcosm experiments, adding five different AHLs to bacterial communities sampled in coastal waters (during early and peak bloom) and monitoring their impact on enzymatic activities and diversity over 48 h. Several specific enzymatic activities were impacted during both experiments, as early as 6 h after the AHL amendments. The BCC was also significantly impacted by the treatments after 48 h, and correlated with the expression of the hydrolytic activities, suggesting that changes in hydrolytic intensities may drive changes in BCC. Overall, our results suggest that QS communication could participate in structuring both the function and diversity of marine bacterial communities.