Critical Role In Biogeochemical Cycling Research Articles

Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist

Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.

Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China

Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.

Pollutant impacts on bacteria in surface water and sediment: Conventional versus emerging pollutants in Taihu Lake, China

Bacteria play a critical role in biogeochemical cycling, self-purification, and food web fueling in surface freshwater ecosystems. However, the comparison between the impacts of conventional and emerging pollutants on the bacteria in surface water and sediment remains unclear and requires for an in-depth understanding to assess ecological risk and select associated bioindicators. Taihu Lake, a typical shallow lake in China, was divided into pollutant impacted and less-impacted zones for sampling. Spatial distributions of conventional pollutants, emerging pharmaceuticals, and bacterial communities were investigated in surface water and sediment. The correlations of pollutants with bacterial communities and the variations in bacterial functions were analyzed to help assess the pollutant influences on bacteria. The results showed that the water quality index and trophic level index across the whole lake were at medium to good, and mesotropher to light eutropher grades, respectively, indicating a relatively good control on conventional pollutants in water. Target pharmaceuticals were at much higher concentrations in water of the impacted zone compared to the less-impacted zone, exhibiting close positive relationships with the bacterial phyla in the impacted water. The ratio of Firmicutes to Proteobacteria in surface water is suggested as a plausible bioindicator to evaluate the level of inflow pharmaceutical contamination and the risk of relevant bacterial resistance in the outflow. In sediment, no significant difference was observed for pharmaceuticals between the two zones, whereas total phosphorus and orthophosphate were substantially higher in the impacted zone. Phosphorus pollutants were tightly associated with the bacterial genera in the impacted sediment, likely relating to the increase in iron- or sulfate-reducing bacteria which implies the potential risk of phosphorus releasing from sediment to water.

Aquatic Macrophytes Are Associated With Variation in Biogeochemistry and Bacterial Assemblages of Mountain Lakes.

In aquatic systems, microbes likely play critical roles in biogeochemical cycling and ecosystem processes, but much remains to be learned regarding microbial biogeography and ecology. The microbial ecology of mountain lakes is particularly understudied. We hypothesized that microbial distribution among lakes is shaped, in part, by aquatic plant communities and the biogeochemistry of the lake. Specifically, we investigated the associations of yellow water lilies (Nuphar polysepala) with the biogeochemistry and microbial assemblages within mountain lakes at two scales: within a single lake and among lakes within a mountain range. We first compared the biogeochemistry of lakes without water lilies to those colonized to varying degrees by water lilies. Lakes with >10% of the surface occupied by water lilies had lower pH and higher dissolved organic carbon than those without water lilies and had a different microbial composition. Notably, cyanobacteria were negatively associated with water lily presence, a result consistent with the past observation that macrophytes outcompete phytoplankton and can suppress cyanobacterial and algal blooms. To examine the influence of macrophytes on microbial distribution within a lake, we characterized microbial assemblages present on abaxial and adaxial water lily leaf surfaces and in the water column. Microbial diversity and composition varied among all three habitats, with the highest diversity of microbes observed on the adaxial side of leaves. Overall, this study suggests that water lilies influence the biogeochemistry and microbiology of mountains lakes.

Spatial and temperal patterns in bacterioplankton communities across a river-lake continuum

Bacterioplankton play critical roles in biogeochemical cycling. Although spatial and temporal variations in bacterioplankton community compositions (BCCs) within individual habitat have been reported, knowledge gaps remain for studies conducted within different habitats. In this work, we examined the seasonal and spatial variability of BCCs in Nanfei River and Lake Chaohu which had significant environmental heterogeneity using a high-throughput sequencing technique of 16S rRNA gene amplicons. The results showed that spatial variation has a more obvious impact on the BCCs than seasonal changes. The microbial diversity gradually decreased and BCCs changed obviously along water flow direction from Nanfei River to the western and estern parts of Lake Chaohu over all seasons. LEfSe analysis showed that Nanfei River had higer abundance of species belonging to the orders Rhodocyclales, Methylococcales, Campylobacterales and Flavobacteriales, samples from eastern part of Lake Chaohu were abundant in taxonomies including the order Rickettsiales, while the western part had high abundance of taxonomies belonging to the order Chroococcales. The redundancy analysis (RDA) indicated that BCCs in Nanfei River were associated with high nutrient (TP, PO4-P, TN, NH3-N, NO2-N and NO3-N) concentrations and electrical conductivity. Variance partitioning RDA analysis indicated that the combined effects of all variables may be most important affecting BCCs. This study may provide a framework for modeling the change in bacterioplankton communities through different habitats from a river to lake.

Dark Ammonium Transformations in the Pearl River Estuary During Summer

AbstractGrowing human activities in recent decades have collectively resulted in large amounts of nutrients export into coastal oceans. As the most reactive nitrogen species, ammonium ( ) plays the critical role in biogeochemical cycles in estuaries and the coastal ocean. In the highly polluted Pearl River Estuary (PRE), predominates to be the energy source for nitrification and to be the material source for bacteria and phytoplankton to grow. Both above processes are affected by light, yet in opposite ways. Nevertheless, rare studies paid attention to dual transformation processes specifically during dark conditions. By using nitrogen isotope tracer technique, we quantitatively and simultaneously differentiated two distinctive consumption pathways, that is, oxidation (AOD) and assimilation (AAD) rates, especially under dark conditions along the PRE during the 2015 and 2017 summer cruises when biological activities were the highest. We found the transformations display a bilayer structure with AAD > AOD in almost all the surface waters and vice versa in all bottom waters, suggesting bacteria and phytoplankton (mainly bacteria) control consumption in surface during the night while nitrifiers are the major consumer in the bottom waters. Through redundancy analysis, we found that both processes are mainly driven by in the PRE during summer. In addition, in the downstream PRE during two cruises, AOD at most contributed 27% and 8% of the water column community dissolved oxygen (DO) consumption assuming the Redfield stoichiometry has no direct effect on hypoxia formation in the PRE during summer.

Dynamics of bacterioplankton community structure in response to seasonal hydrological disturbances in Poyang Lake, the largest wetland in China.

Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang Lake, the largest seasonal freshwater lake in China. Our results revealed no overall difference in bacterioplankton compositions and their predicted functions among spatially separated sites. However, bacterioplankton communities did show significant temporal shifts, mainly between samples in November and other months. Transitions from the dry to the wet season were observed in October in both sampling years. Meanwhile, insignificant spatial but significant temporal differences were also found for physicochemical variables. Moreover, redundancy analysis indicates that compared with water depth, water temperature was found to better explain changes in the bacterioplankton community. These findings consistently indicate that the bacterioplankton community in Poyang Lake is relatively less sensitive to annual hydrology shifts than water temperature and nutrient conditions.

Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality

Biodiversity on the Earth is changing at an unprecedented rate due to a variety of global change factors (GCFs). However, the effects of GCFs on microbial diversity is unclear despite that soil microorganisms play a critical role in biogeochemical cycling. Here, we synthesize 1235 GCF observations worldwide and show that microbial rare species are more sensitive to GCFs than common species, while GCFs do not always lead to a reduction in microbial diversity. GCFs-induced shifts in microbial alpha diversity can be predominately explained by the changed soil pH. In addition, GCF impacts on soil functionality are explained by microbial community structure and biomass rather than the alpha diversity. Altogether, our findings of GCF impacts on microbial diversity are fundamentally different from previous knowledge for well-studied plant and animal communities, and are crucial to policy-making for the conservation of microbial diversity hotspots under global changes.

Broadband acoustic quantification of mesopelagic zooplankton

In addition to its critical role in biogeochemical cycling, the mesopelagic zone has the potential to become an important global fisheries resource. A growing number of studies have focused on estimating the global biomass of mesopelagic fishes, but that of mesopelagic zooplankton is far more uncertain. Yet, quantification of zooplankton biomass and distribution is crucial to both understanding the ecology of the mesopelagic zone and informing policy makers on sustainable exploitation. Shipboard, narrowband, volume backscattering measurements—typically performed at 18 and/or 38 kHz—are likely dominated by gas-bearing organisms, hindering accurate assessment of zooplankton biomass. A towed vehicle, Deep-See, was developed and equipped with broadband acoustics from 1–450 kHz, optical sensors, and environmental sensors to address the challenges associated with systematically acquiring holistic, quantitative data to infer mesopelagic biomass. Broadband backscattering spectra (50–160 kHz) collected by Deep-See in Summer 2018 and 2019 off the New England shelf break are used to classify scattering layers into fluid-like zooplankton (e.g., jellies, copepods, krill) or gas-bearing organisms (e.g., fishes, siphonophores), then physics-based scattering models are used to estimate abundance and biomass. Consistent with the acoustic measurements, digital holographic images collected by Deep-See reveal multiple deep scattering layers, some consisting mainly of weakly scattering krill.

In situ detection of microbial c-type cytochrome based on intrinsic peroxidase-like activity using screen-printed carbon electrode

C-type cytochromes (c-cyts) facilitate microbial extracellular electron transfer and play critical roles in biogeochemical cycling, bioelectricity generation and bioremediation. In this study, a simple and effective method has been developed to detect microbial c-cyts by means of peroxidase mimetic reaction on screen-printed carbon electrode (SPCE). To this end, bacteria cells were immobilized onto the working electrode surface of SPCE by a simple drop casting. After introducing 3,3′,5,5′-tetramethylbenzidine (TMB) solution, microbial c-cyts with peroxidase-like activity catalyze the oxidation of TMB in the presence of hydrogen peroxide. The oxidized TMB was electrochemically determined and the current signal was employed to calculate the c-cyts content. This electrochemical method is highly sensitive for microbial c-cyts with a low detection limit of 40.78 fmol and a wide detection range between 51.70 fmol and 6.64 pmol. Moreover, the proposed technique can be universally expanded to detect c-cyts in other bacteria species such as Fontibacter ferrireducens, Pseudomonas aeruginosa, Comamonas guangdongensis and Escherichia coli. Furthermore, the proposed method confers an in situ facile and quantitative c-cyts detection without any destructive sample preparations, complex electrode modifications and expensive enzyme- or metal particle- based signal amplification. The suggested method advances an intelligent strategy for in situ quantification of microbial c-cyts and consequently holds promising application potential in microbiology and environmental science.

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition

Sediment bacterial communities play a critical role in biogeochemical cycling in lotic ecosystems. Despite their ecological significance, the effects of urban discharge on spatiotemporal distribution of bacterial communities are understudied. In this study, we examined the effect of urban discharge on the spatiotemporal distribution of stream sediment bacteria in a northeast Ohio stream. Water and sediment samples were collected after large storm events (discharge > 100 m) from sites along a highly impacted stream (Tinkers Creek, Cuyahoga River watershed, Ohio, USA) and two reference streams. Although alpha (α) diversity was relatively constant spatially, multivariate analysis of bacterial community 16S rDNA profiles revealed significant spatial and temporal effects on beta (β) diversity and community composition and identified a number of significant correlative abiotic parameters. Clustering of upstream and reference sites from downstream sites of Tinkers Creek combined with the dominant families observed in specific locales suggests that environmentally-induced species sorting had a strong impact on the composition of sediment bacterial communities. Distinct groupings of bacterial families that are often associated with nutrient pollution (i.e., Comamonadaceae, Rhodobacteraceae, and Pirellulaceae) and other contaminants (i.e., Sphingomonadaceae and Phyllobacteriaceae) were more prominent at sites experiencing higher degrees of discharge associated with urbanization. Additionally, there were marked seasonal changes in community composition, with individual taxa exhibiting different seasonal abundance patterns. However, spatiotemporal variation in stream conditions did not affect bacterial community functional profiles. Together, these results suggest that local environmental drivers and niche filtering from discharge events associated with urbanization shape the bacterial community structure. However, dispersal limitations and interactions among other species likely play a role as well.

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor.

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to "cross-feeding" with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were "cross-fed" with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.

Submerged aquatic vegetation, topography and flow characteristics in the upper, tidal Hudson River: Progress toward a predictive habitat model

Submerged aquatic vegetation (SAV) plays a critical role in biogeochemical cycling, primary productivity, sediment dynamics and current flow within the systems they inhabit. SAV communities in the Upper Hudson River Estuary are comprised of species assemblages dominated by two very morphologically distinct species: the native Vallisneria americana, which has wide-strap shaped leaves that are completely submerged underwater, and the invasive Trapa natans, which produces leaf rosettes that float at the water’s surface. Using characteristics of modeled tidal/riverine flow, we examined the distribution and composition of the predominant SAV in the estuary. SAV habitat space was, on average, well described by depth and flow. From a hydrodynamic standpoint however, the two species occupied very similar niche spaces. Species-specific distribution patterns and co-occurrence rates did not appear to be strongly controlled by physical tolerances of topography or flow. Other ecological drivers such as disturbance regimes, dispersal strategies, plant-animal interactions, and sediment chemistry and composition might explain distribution patterns and T. natans expansion more accurately, rather than hydrodynamics alone. Sixty years after reaching the Hudson River Estuary, T. natans appears unable to fully displace V. americana, despite significant overlap in habitat space and spatial distribution. Future management of the exotic T. natans should consider its role as an ecosystem engineer, adding to overall habitat diversity, rather than the current focus on its perceived invasibilty.

Soil organic phosphorus transformation during ecosystem development: A review

Soil organic phosphorus transformation during ecosystem development exerts a crucial influence on soil fertility and ecosystem properties. This paper reviews the use of solution 31P NMR spectroscopy for characterizing organic phosphorus speciation in soil chronosequence and long-term field experiments in order to improve our understanding of the temporal changes, fundamental processes, and associated natural and anthropogenic controls of organic phosphorus transformation during long-term ecosystem evolution. Published soil chronosequence studies show that organic phosphorus compounds under aerobic conditions are dominated by phosphate monoesters (occurred mainly as inositol phosphates) followed by phosphate diesters (occurred mainly as DNA) and phosphonates, irrespective of the different parent materials, vegetation covers and climatic conditions. This contrasted markedly with wetland soils in which phosphate monoesters and diesters maintained approximately equal proportions, which is attributed to the limited reactive clay surfaces for stabilization and/or decomposition of myo-inositol hexakisphosphate under frequent anaerobic conditions. Most organic phosphorus compounds in soil chronosequences increase with age to reach a maximum and then decline with time, although the apex varies significantly among different organic phosphorus compounds and chronosequences. Variations of the potential for phosphorus stabilization resulting from mineralogical transformation, changes in phosphorus sources due to shifts in plant and microbial communities, and differences in the biological utilization of various phosphorus compounds have been suggested as three main mechanisms controlling the temporal changes in organic phosphorus species, abundance and availability during natural ecosystem development. In agricultural soils, the amounts, forms, and dynamics of organic phosphorus are determined by internal soil properties, external environmental conditions and managements, including the history and intensity of land use, different tillage practices and fertilizer treatments. These mechanisms are interlinked and more research is required to isolate both internal and external factors that regulate organic phosphorus transformation in agricultural ecosystems. Given the universal dependence on organic phosphorus for life and its critical roles in biogeochemical cycling, we put forward several open questions that need to be resolved in the future studies by emphasizing the multidisciplinary collaborations, the use of multiple analytical techniques and the establishment of quantitative organic phosphorus transformation models.

Southern Ocean Phytoplankton in a Changing Climate

Phytoplankton are the base of the Antarctic food web, sustain the wealth and diversity of life for which Antarctica is renowned, and play a critical role in biogeochemical cycles that mediate global climate. Over the vast expanse of the Southern Ocean (SO), the climate is variously predicted to experience increased warming, strengthening wind, acidification, shallowing mixed layer depths, increased light (and UV), changes in upwelling and nutrient replenishment, declining sea ice, reduced salinity, and the southward migration of ocean fronts. These changes are expected to alter the structure and function of phytoplankton communities in the SO. The diverse environments contained within the vast expanse of the SO will be impacted differently by climate change; causing the identity and the magnitude of environmental factors driving biotic change to vary within and among bioregions. Predicting the net effect of multiple climate-induced stressors over a range of environments is complex. Yet understanding the response of SO phytoplankton to climate change is vital if we are to predict the future state/s of the ecosystem, estimate the impacts on fisheries and endangered species, and accurately predict the effects of physical and biotic change in the SO on global climate. This review looks at the major environmental factors that define the structure and function of phytoplankton communities in the SO, examines the forecast changes in the SO environment, predicts the likely effect of these changes on phytoplankton, and considers the ramifications for trophodynamics and feedbacks to global climate change. Predictions strongly suggest that all regions of the SO will experience changes in phytoplankton productivity and community composition with climate change. The nature, and even the sign, of these changes varies within and among regions and will depend upon the magnitude and sequence in which these environmental changes are imposed. It is likely that predicted changes to phytoplankton communities will affect SO biogeochemistry, carbon export, and nutrition for higher trophic levels.

Long-term environmental drivers of DOC fluxes: Linkages between management, hydrology and climate in a subtropical coastal estuary

Urban and agricultural development of the South Florida peninsula has disrupted historic freshwater flow in the Everglades, a hydrologically connected ecosystem stretching from central Florida to the Gulf of Mexico, USA. Current system-scale restoration efforts aim to restore natural hydrologic regimes to reestablish pre-drainage ecosystem functioning through increased water availability, quality and timing. Aquatic transport of carbon in this ecosystem, primarily as dissolved organic carbon (DOC), plays a critical role in biogeochemical cycling and food-web dynamics, and will be affected both by water management policies and climate change. To better understand DOC dynamics in South Florida estuaries and how hydrology, climate and water management may affect them, 14 years of monthly data collected in the Shark River estuary were used to examine DOC flux dynamics in a broader environmental context. Multivariate statistical methods were applied to long-term datasets for hydrology, water quality and climate to untangle the interconnected environmental drivers that control DOC export at monthly and annual scales. DOC fluxes were determined to be primarily controlled by hydrology but also by seasonality and long-term climate patterns and episodic weather events. A four-component model (salinity, rainfall, inflow, Atlantic Multidecadal Oscillation) capable of predicting DOC fluxes (R2 = 0.84, p < 0.0001, n = 155) was established and applied to potential climate change scenarios for the Everglades to assess DOC flux response to climate and restoration variables. The majority of scenario runs indicated that DOC export from the Everglades is expected to decrease due to future changes in rainfall, water management and salinity.

Arctic soil microbial diversity in a changing world

The Arctic region is a unique environment, subject to extreme environmental conditions, shaping life therein and contributing to its sensitivity to environmental change. The Arctic is under increasing environmental pressure from anthropogenic activity and global warming. The unique microbial diversity of Arctic regions, that has a critical role in biogeochemical cycling and in the production of greenhouse gases, will be directly affected by and affect, global changes. This article reviews current knowledge and understanding of microbial taxonomic and functional diversity in Arctic soils, the contributions of microbial diversity to ecosystem processes and their responses to environmental change.

Assessing sediment toxicity: Past, present, and future

Assessing sediment toxicity: Past, present, and future