Lake Communities Research Articles

Fish size structures in lakes of the Lower Mississippi River floodplain

Abstract The Lower Mississippi River has a floodplain that includes >1350 perennial lakes carved by shifts in river courses and other hydro‐fluvial processes over eons. Notwithstanding their similar provenances, these waterbodies exhibit an immense variety of morphologies and successional stages that illustrate their natural trajectory from aquatic to forested wetlands. A result of this geographical, morphological and temporal diversity is dynamic and varied fish communities. We examined how size structures of fish communities in these floodplain lakes were associated with key in‐lake and off‐lake environmental drivers. Fish lengths were collected with standardised procedures in a sample of 30 of these lakes to construct a lake‐by‐length group matrix. Likewise, in‐lake and off‐lake environmental descriptors were collected to construct a lake‐by‐covariate matrix. Distance‐based linear models were used to assess associations between fish size structure and environmental descriptors. Smaller fish were typically associated with increasing levels of turbidity, chlorophyll‐a, phycocyanin and surrounding agriculture. Shallow, hypereutrophic floodplain lakes associated with agricultural landscapes and reduced connectivity experience harsh physicochemical environments. These conditions appeared to hinder the formation of sustained fish communities but may confer a survival advantage to juveniles or small short‐lived species. Conversely, larger fish were associated with increasing lake depth, water clarity, connectivity, and extent of surrounding forests‐wetlands. Enhanced stability and size structure were observed in communities residing in deeper and clearer lakes, suggesting that these conditions facilitated the development of longer‐lived species spanning multiple age groups. The enhanced connectivity that facilitated this increased stability also permitted the presence of larger itinerant species. Size‐structure assessments can serve as a valuable ecological and biodiversity indicator in floodplain lakes. Size‐structure assessments could supplement and, depending on objectives, even supplant conventional taxonomic analyses, and enhance surveillance of this vast and important natural resource.

Variation of the sediment denitrifying bacterial community in a floodplain lake (Poyang Lake, China) during the wet, mid-dry and dry seasons

Variation of the sediment denitrifying bacterial community in a floodplain lake (Poyang Lake, China) during the wet, mid-dry and dry seasons

Ecohydrological changes recorded by sedimentary diatoms in the Dajiuhu Wetland in Shennongjia over the past 40 years.

Anthropogenic hydrological regulation is profoundly altering the structure and function of wetland ecosystems. Due to the scarcity of long-term monitoring records, the responses of wetland ecosystems to anthropogenic hydrological regulation remain unclear. We reconstructed past ecohydrological changes in Dajiuhu Wetland during the last 40 years and explored the driving forces, based on multiproxy records of a 44-cm-length sediment core collected from Wuhaohu Lake of Dajiuhu Wetland in Shennongjia, Hubei. The results showed that the diatom community in Wuhaohu Lake had experienced three major stages, including the dominance of benthic diatoms between 1980 and 2008, the rapid increase in planktonic diatoms between 2008 and 2016, and the dominance of small-sized fragilarioid species after 2016. Results of redundancy analysis showed that change in diatom assemblage was significantly correlated with total organic carbon, total nitrogen and the ratios of Mn to Fe. Diatom floral changes after 2008 indicated the shift of Wuhaohu Lake from an early organic-rich peatland to a shallow lake, mainly in response to an increase in water table driven by damming. From 2016, the increases in benthic and epiphytic diatoms responded to the expansion of aquatic plants and improved light penetration after the relocation of local population. Sedimentary diatom records revealed the process of environmental changes, and hence would provide a scientific basis for the environmental protection of wetlands.

In search of the pH limit of growth in halo-alkaliphilic cyanobacteria.

Cyanobacteria have many biotechnological applications. Increasing their cultivation pH can assist in capturing carbon dioxide and avoiding invasion by other organisms. However, alkaline media may have adverse effects on cyanobacteria, such as reducing the Carbon-Concentrating Mechanism's efficiency. Here, we cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that increasing the pH decreased biomass yield. This decrease was caused, in part, by a dramatic increase in carbon transfer to heterotrophs. At pH 11.4, cyanobacterial growth became limited by bicarbonate uptake, which was mainly ATP dependent. In parallel, the higher the pH, the more sensitive cyanobacteria became to light, resulting in photoinhibition and upregulation of DNA repair systems.

Lake Champlain Zooplankton Community Dynamics Following an Extreme Flood Event

Lake Champlain, the sixth largest freshwater lake in the U.S., is a deep thermally stratified temperate zone lake system. Recently, flood events have impacted the Northeastern U.S. more frequently than in past decades, resulting in increased turbidity and other impacts in northern temperate lakes. This study represents an unprecedented analysis of the impacts of major spring and summer flooding in 2011 on Lake Champlain zooplankton communities. Few studies exist on flood impacts on lake systems, especially in natural un-impounded lakes. Our results illustrate the impacts of large-scale flooding on planktonic communities in deep stratified temperate lakes and the differential responses among species based on autecological traits. Community responses include flood-adapted increase during the flood event (Ceriodaphnia reticulata and Eubosmina coregoni), a flood-intolerant decline (Asplanchna spp. and Keratella cochlearis) or a delayed flood intolerance (Daphnia retrocurva, Mesocyclops edax, and Polyarthra spp.). Our results suggest that large, temperate lakes such as Lake Champlain will experience community shifts in zooplankton composition during future extreme flood events associated with climate change-related weather patterns in the Northeastern U.S.

Principal determinants of aquatic macroinvertebrate communities in small shallow lakes and ponds

Principal determinants of aquatic macroinvertebrate communities in small shallow lakes and ponds

Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake

In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.

Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake.

Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.

Year-round sampling of the fish community in a boreal lake: differences between summer and winter influence estimates of species composition, catch, and fish size.

Boreal lakes experience pronounced seasonal variation in abiotic factors, especially light, temperature, and oxygen. A deep boreal humic lake was sampled year-round to test putative changes in total fish catch, species composition, catch-per-unit-effort (CPUE), habitat use, fish size, and condition. Monthly sampling was conducted in Lake Pääjärvi, southern Finland, during one full year in 2020-2021 as well as in March and August 2021 and 2022. The fish community was dominated by cyprinid species in all months, but the percentage of percid fish caught increased during the warm summer period. Most fish were caught in littoral habitats and the highest catches occurred in summer, but some species (e.g., ruffe, Gymnocephalus cernua, and pikeperch, Sander lucioperca) remained abundant in the winter catch. The body size of fish was larger in the winter catch, while condition factor was higher in summer for most species. Fish species proportions in total catch, CPUE, and average size of fish were closest to the annual mean values in September, which may be used as the optimal period to monitor fish communities of similar deep boreal lakes. Our findings highlight the need for year-round research to reveal the impacts of rising temperatures and diminishing ice-covered periods in fish communities and lake food webs.

Heterogenization of microplastic communities in lakes of the Qinghai-Tibetan Plateau driven by tourism and transport activities

The Qinghai-Tibetan Plateau has a booming tourism industry and an increasingly sophisticated road system. There is a paucity of studies quantifying the contributions of anthropogenic and natural factors to microplastic pollution in remote plateau areas. In this study, water and sediment samples were collected from eight lake tourist attractions and four remote lakes in northern and southern regions of the Qinghai-Tibetan Plateau. Microplastics were detected in all samples, with a mean abundance of 0.78 items/L in water and 44.98 items/kg in sediment. The abundance of microplastics in the study area was lower than previously observed in more populated areas of China. Small-sized (<1 mm and 1–2 mm), fiber, and transparent microplastics were predominant, with polyethylene and polypropylene microplastics as the primary polymer types. The compositions of microplastic communities indicated that tourism and road networks were the major sources of microplastics in the lakes. Distance-decay models revealed greater influence of environmental distances on microplastic community similarity than geographic distance. Compared to climate factors, urban spatial impact intensity and traffic flow impact played a leading role in the structuring of microplastic communities in lake water and sediment. Our findings provide novel quantitative insights into the role of various factors in shaping the distribution patterns of microplastic communities in plateau lakes.

Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China.

Volcanic lakes originate from a volcanic crater or caldera, and were a crucial component of aquatic ecosystems. Sediment bacteria play an important role in the nutrient cycling of aquatic ecosystems; however, their patterns distribution in volcanic lakes and the surrounding river habitats are unknown. In this study, we compare the sediment bacterial communities and their co-occurrence networks between these two habitats in the Inner Mongolia Autonomous Region, Northeastern China (the Arxan UNESCO Global Geopark), using 16S rRNA gene amplicon sequencing. The results revealed that there were significant variations in the physicochemical parameters of the sediment between these two habitats. The bacterial α-diversity, β-diversity, and community composition of the sediment also significantly differed between these two habitats. Network analysis showed that the co-occurrence patterns and keystone taxa in the sediment differed between these two habitats. The sediment bacterial communities in the river habitats were more stable than those in the lake habitats in the face of environmental change. Canonical correspondence analysis demonstrated that both physical (pH and MC) and nutrition-related factors (TN, TP, LOI, and TOC) were the most important environmental factors shaping the variations of bacterial community composition (BCC) in the sediment between these two habitats. This work could greatly improve our understanding of the sediment BCC of the sediment from aquatic ecosystems in the UNESCO Global Geopark.

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning.

Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.

The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.

The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.

Eutrophication impacts the distribution and functional traits of viral communities in lakes

Viruses play a crucial role in aquatic ecosystems by regulating microbial composition and impacting biogeochemical cycling. While the response of viral diversity to the trophic status has been preliminarily explored in lake ecosystems, there is limited integrated exploration of the biogeography of viruses, host associations, and the auxiliary metabolic genes (AMGs), particularly for plateau lakes. Therefore, this research investigated the viral biogeography, virus-host association, and AMGs in the surface waters of 11 lakes varying in trophic levels (eutrophic and oligo-mesotrophic) in the Yunnan-Guizhou plateau region of China. A total of 73,105 viral operational taxonomic units were obtained from 11 samples, with 84.8 % remaining unannotated at the family level, indicating a predominance of novel viruses within these lakes. The most abundant viral family was Kyanoviridae (24.4 %), recognized as a common cyanophage. The vast majority of cyanobacteria and several eukaryotic algae were predicted as hosts for the viruses, with a lytic lifestyle predominating the life strategy of these cyanophages, implying the potential influence of the virus on algae. The viral community structure significantly correlated with both trophic status and the bacterial community. The structure equation model analysis revealed chlorophyll a was the primary factor affecting viral communities. Moreover, numerous AMGs linked to carbon metabolism, phosphorus metabolism, sulfur metabolism, and photosynthesis were found in these lakes, some of which showed virus preference for the trophic statuses, suggesting a vital role of the virus in driving biogeochemical cycling in the lake crossing different nutrient levels. In addition, a restricted presence of viruses was found to infect humans or harbor antibiotic resistance genes in the lakes, suggesting a subtle yet potential link to human health. Overall, these findings offer insights into the response of viral communities to eutrophication and their potential role in biogeochemical cycling and controlling algal propagation.

Citizen perceptions of Great Lakes coastline change and management efforts

Fluctuating water levels, nearshore flooding and associated coastal erosion present management challenges for coastal communities around the world. Along the Great Lakes, integrated coastal zone management efforts involve a complex array of people and institutions, which include citizens of coastal communities. At this point in time, there are few studies focused on community members' perceptions of and views on current management efforts on the Great Lakes. To address this need, the present study analyzes survey data from the public and six Great Lake communities with three objectives in mind. One, to understand perceptions of the causes of coastline change and the hazards associated with these changes. Two, to understand the consequences of coastline change for people and the greater community. Three, to understand citizens’ viewpoints about different strategies for managing coastline changes and the parties responsible for managing the coastline. Study results indicate conflicting perceptions between community members about common coastline management efforts (e.g. armoring, beach nourishment, and setbacks). They also indicate a general lack of knowledge about the complexities and responsible parties for coastline management, which in some cases, may be individual property owners themselves. The results of this study suggest efforts to educate citizens may be critical for future stewardship of the Great Lakes, which requires community partnerships and buy in to be successful.

From disruption to adaptation: Response of phytoplankton communities in representative impounded lakes to China's South-to-North Water Diversion Project

Impounded lakes are often interconnected in large-scale water diversion projects to form a coordinated system for water allocation and regulation. The alternating runoff and transferred water can significantly impact local ecosystems, which are initially reflected in the sensitive phytoplankton. Nonetheless, limited information is available on the temporal dynamics and assembly patterns of phytoplankton community in impounded lakes responding to continuous and periodic water diversion. Herein, a long-term monitoring from 2013 to 2020 were conducted to systematically investigate the response of phytoplankton community, including its characteristics, stability, and the ecological processes governing community assembly, in representative impounded lakes to the South-to-North Water Diversion Project (SNWDP) in China. In the initial stage of the SNWDP, the phytoplankton diversity indices experienced a decrease during both non-water diversion periods (8.5 %∼21.2 %) and water diversion periods (5.6 %∼12.2 %), implying a disruption in the aquatic ecosystem. But the regular delivery of high-quality water from the Yangtze River gradually increased phytoplankton diversity and mediated ecological assembly processes shifting from stochastic to deterministic. Meanwhile, reduced nutrients restricted the growth of phytoplankton, pushing species to interact more closely to maintain the functionality and stability of the co-occurrence network. The partial least squares path model revealed that ecological process (path coefficient = 0.525, p < 0.01) and interspecies interactions in networks (path coefficient = -0.806, p < 0.01) jointly influenced the keystone and dominant species, ultimately resulting in an improvement in stability (path coefficient = 0.878, p < 0.01). Overall, the phytoplankton communities experienced an evolutionary process from short-term disruption to long-term adaptation, demonstrating resilience and adaptability in response to the challenges posed by the SNWDP. This study revealed the response and adaptation mechanism of phytoplankton communities in impounded lakes to water diversion projects, which is helpful for maintaining the lake ecological health and formulating rational water management strategies.

Factors of macrozoobenthos formation in low-mountain lakes of the Russian Altai

The current state of macrozoobenthos of six low-mountain lakes of the Russian Altai was studied in different hydrological seasons (May, July, September) 2022: Aya (Aiskoe), Beloe, Kireevo, Kolyvanskoe, Koksha, and Svetloe. The aim of the article is to study the factors of formation of benthic invertebrate communities of foothill lakes of the Russian Altai. In total 156 species from 9 classes of invertebrates were identified in the zoobenthos of the studied lakes, the highest percentage of occurrence was recorded for chironomids and oligochaetes. According to the taxonomic composition of macrozoobenthos, most of the studied lakes of the Russian Altai (Aya, Beloe, Kireevo and Kolyvanskoe) were close to flatland lakes. Two lakes (Koksha and Svetloe) combined characteristics of both flatland and highland lakes. The abundance and biomass of zoobenthos in lakes Aya and Kireevo corresponded to the oligotrophic level, in lakes Beloe and Kolyvanskoe to the mesotrophic level, and in lakes Koksha and Svetloye to the eutrophic level. The structural characteristics of macroinvertebrates are indicators of the state of lake ecosystems. Therefore, in order to maintain the health of lake ecosystems, it is important to determine the limiting factors for macroinvertebrate community composition and structure. The influence of environmental factors on the composition and structure of macrozoobenthos of foothill lakes of the Russian Altai was studied. The relationship of 10 main indicators of zoobenthos structure with 30 hydro physical and hydrochemical indicators was analyzed. Using principal component analysis, multiple regression method, correlation and canonical analyses, it was revealed that the greatest influence on the development of benthic invertebrate communities in the studied lakes of the Russian Altai was exerted by nutrients, permanganate oxidability and soil character and water temperature.

Determination of the Microorganisms’ Resistance to Antibiotics in the Bacterioplankton Community in the Akmola Region Lakes

Determination of the Microorganisms’ Resistance to Antibiotics in the Bacterioplankton Community in the Akmola Region Lakes

Brownification increases the abundance of microorganisms related to carbon and nitrogen cycling in shallow lakes

Brownification in aquatic ecosystems under global change has attracted attention. The composition and quantity of dissolved organic matter transported from various land use types to lakes differ significantly, causing varying ecological effects of lake brownification by region. Bacterial communities make a significant contribution to the material cycle of ecosystems and are sensitive to environmental changes. In this study, a series of mesocosm systems were used to simulate forest lakes and urban lakes with different degrees of brownification, and a high-throughput amplicon sequencing technique was used to explore the changes in the composition, structure, and function of bacterial communities in shallow lakes undergoing brownification. Principal coordinate analysis (PCoA) and Jensen‒Shannon distance typing analysis both indicated significant differences in bacterial communities between forest lakes and urban lakes. The α diversity of bacterial communities in urban lakes increased with the degree of brownification. However, whether forest lakes or urban lakes, brownification increased the abundance of carbon cycling-related bacterial phyla (Proteobacteria, Poribacteria, and Chloroflexi) and nitrogen cycling-related bacterial genera (Microbacteriaceae, Limnohabitans, Comamonadaceae, Bacillus, and Rhizobiales_Incertae_Sedis). Additionally, the carbon and nitrogen cycling functions of bacterial communities in forest lakes are dominant, while those in urban lakes are dominated by functions related to light. Our study has preliminarily revealed that lake brownification promotes the growth of carbon and nitrogen cycling microorganisms, providing a new paradigm for understanding the response of lake ecosystems in different catchment areas to environmental changes and the carbon and nitrogen cycling processes in shallow lake ecosystems.

Submerged macrophyte restoration enhanced microbial carbon utilization in shallow lakes

Submerged macrophytes are integral to the functioning of shallow lakes through their interaction with microorganisms. However, we have a limited understanding of how microbial communities in shallow lakes respond when macrophytes are restored after being historically extirpated. Here, we explored the interactions between prokaryotic communities and carbon utilization in two lakes where submerged macrophytes were restored. We found restoration reduced total carbon in sediment by 8.9 %–27.9 % and total organic carbon by 16.7 %–36.9 % relative to control treatment, but had no effects on carbon content in the overlying water. Sediment microbial communities were more sensitive to restoration than planktonic microbes and showed enhanced utilization of simple carbon substrates, such as Tween 40, after restoration. The increase in carbon utilization was attributed to declines in the relative abundance of some genera, such as Saccharicenans and Desertimonas, which were found weakly associated with the utilization of different carbon substrates. These genera likely competed with microbes with high carbon utilization in restored areas, such as Lubomirskia. Our findings highlight how restoring submerged macrophytes can enhance microbial carbon utilization and provide guidance to improve the carbon sequestration capacity of restored shallow lakes.