Search Results (11)

Groundwater, a critical source of drinking water, plays an essential role in global biogeochemical cycles, yet its microbial ecosystems remain insufficiently characterized, particularly in pristine karst aquifers. This study conducted high-resolution profiling of microbial communities and environmental parameters in two representative alpine karst aquifers in Slovenia: Idrijska Bela and Krajcarca. Monthly groundwater samples from the Krajcarca spring and Idrijska Bela borehole over a 14-month period were analyzed using whole-metagenome sequencing (WMS), UV-Vis spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), and isotopic analysis. The results revealed stable hydrochemical conditions with clear spatial differences driven by bedrock composition and groundwater residence time. Bacterial communities displayed strong correlations with hydrochemical parameters, while archaeal communities exhibited temporal stability. Functional gene profiles mirrored bacterial patterns, emphasizing the influence of environmental gradients on metabolic potential. No significant temporal changes were detected across two sampling campaigns (2016–2023), highlighting the resilience of these aquifers. This work establishes a valuable baseline for understanding pristine groundwater microbiomes and informs future monitoring and water quality management strategies. Full article

Water scarcity is a major agricultural issue in most arid and semi-arid regions of the world. Alternative water supplies, such as the reuse of wastewater for agricultural irrigation, have been introduced. However, little is known about their impact on the soil and rhizosphere microbiomes that receive irrigation. Therefore, this work evaluates the impact of treated wastewater (TWW) irrigation on the soil and rhizosphere bacterial communities of date palms in Al Madinah, Saudi Arabia. In this study, metagenomic DNA from the rhizosphere of the date palm was sequenced using Illumina high-throughput sequencing. According to the observed OTUs, Chao1 richness estimations, and Shannon diversity values, soils from groundwater-irrigated date palms showed higher microbial diversity than did soils from TWW-irrigated date palms. A total of 569 OTUs were generated; most of them (97.3%) were assigned into 15 different phyla, whereas 2.7% were marked as unclassified. DNA sequence analysis of the WWT-irrigated rhizosphere showed that the most abundant phyla were Firmicutes (43.6%), Bacteroidetes (17.3%), Proteobacteria (15.2%), and Actinobacteria (14.6%), representing more than 90.7% of the total community, while the soil of the rhizosphere irrigated with GW was dominated by Actinobacteria (44.1%), Proteobacteria (23.4%), Firmicutes (15.5%), and Gemmatimonadetes (4.9%). The most frequently observed species in the two soils were also different. The dominant species in TWW-irrigated soil was Planococcus plakortidis, which is prevalent in saline and moderately saline habitats and can play an important ecological role. The GW-irrigated rhizosphere exhibited higher levels of biocontrol bacteria, particularly Nocardioides mesophilus. These results provide a comprehensive understanding and insights into the population dynamics and microbiome of date palm rhizosphere. The findings show that the irrigation water quality has a significant impact on the microbiome composition. Identifying the microbial diversity is the first step toward determining the best way to use TWW in irrigation. Full article

Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments. Full article

Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil–Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers. Full article

In drinking water supply, riverbank filtration (RBF) is an efficient and cost-effective way of eliminating pathogens and micropollutants using a combination of biotic and abiotic processes. Microbial communities in the hyporheic zone both contribute to and are shaped by these processes. Microbial water quality at the point of consumption is in turn influenced by the source water microbiome, water treatment and distribution system. Understanding microbial community shifts from source to tap and the factors behind them is instrumental in maintaining safe drinking water delivery. To this end, microbial communities of an RBF-based drinking water supply system were investigated by metabarcoding in a one-year sampling campaign. Samples were collected from the river, RBF wells, treated water, and a consumer’s tap. Metabarcoding data were analysed in the context of physicochemical and hydrological parameters. Microbial diversity as well as cell count decreased consistently from the surface water to the tap. While Proteobacteria were dominant throughout the water supply system, typical river water microbiome phyla Bacteroidota, Actinobacteria, and Verrucomicrobiota were replaced by Nitrospira, Patescibacteria, Chloroflexi, Acidobacteriota, Methylomicrobilota, and the archaeal phylum Nanoarcheota in well water. Well water communities were differentiated by water chemistry, in wells with high concentration groundwater derived iron, manganese, and sulphate, taxa related to iron and sulphur biogeochemical cycle were predominant, while methane oxidisers characterised the more oxic wells. Chlorine-resistant and filtration-associated taxa (Acidobacteria, Firmicutes, and Bdellovibrionota) emerged after water treatment, and no potentially pathogenic taxa were identified at the point of consumption. River discharge had a distinct impact on well water microbiome indicative of vulnerability to climate change. Low flow conditions were characterised by anaerobic heterotrophic taxa (Woesarchaeales, Aenigmarchaeales, and uncultured bacterial phyla MBNT15 and WOR-1), implying reduced efficiency in the degradation of organic substances. High flow was associated the emergence of typical surface water taxa. Better understanding of microbial diversity in RBF water supply systems contributes to preserving drinking water safety in the future changing environment. Full article

Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use. Full article

Soil is a porous matrix containing organic matter and minerals as well as living organisms that vary physically, geographically, and temporally. Plants choose a particular microbiome from a pool of soil microorganisms which helps them grow and stay healthy. Many ecosystem functions in agrosystems are provided by soil microbes just like the ecosystem of soil, the completion of cyclic activity of vital nutrients like C, N, S, and P is carried out by soil microorganisms. Soil microorganisms affect carbon nanotubes (CNTs), nanoparticles (NPs), and a nanopesticide; these are called manufactured nano-objects (MNOs), that are added to the environment intentionally or reach the soil in the form of contaminants of nanomaterials. It is critical to assess the influence of MNOs on important plant-microbe symbiosis including mycorrhiza, which are critical for the health, function, and sustainability of both natural and agricultural ecosystems. Toxic compounds are released into rural and urban ecosystems as a result of anthropogenic contamination from industrial processes, agricultural practices, and consumer products. Once discharged, these pollutants travel through the atmosphere and water, settling in matrices like sediments and groundwater, potentially rendering broad areas uninhabitable. With the rapid growth of nanotechnology, the application of manufactured nano-objects in the form of nano-agrochemicals has expanded for their greater potential or their appearance in products of users, raising worries about possible eco-toxicological impacts. MNOs are added throughout the life cycle and are accumulated not only in the soils but also in other components of the environment causing mostly negative impacts on soil biota and processes. MNOs interfere with soil physicochemical qualities as well as microbial metabolic activity in rhizospheric soils. This review examines the harmful effect of MNOs on soil, as well as the pathways used by microbes to deal with MNOs and the fate and behavior of NPs inside the soils. Full article

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes. Full article

Monitoring bacterial communities in a drinking water treatment plant (DWTP) may help to understand their regular operations. Bacterial community dynamics in an advanced full-scale DWTP were analyzed by 16S rRNA metabarcoding, and microbial water quality indicators were determined at nine different stages of potabilization: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, mixing chamber and post-chlorination drinking water. The microbial content of large water volumes (up to 1100 L) was concentrated by hollow fiber ultrafiltration. Around 10 million reads were obtained and grouped into 10,039 amplicon sequence variants. Metabarcoding analysis showed high bacterial diversity at all treatment stages and above all in groundwater intake, followed by carbon filtration and mixing chamber samples. Shifts in bacterial communities occurred downstream of ozonization, carbon filtration, and, more drastically, chlorination. Proteobacteria and Bacteroidota predominated in river water and throughout the process, but in the final drinking water, the strong selective pressure of chlorination reduced diversity and was clearly dominated by Cyanobacteria. Significant seasonal variation in species distribution was observed in decantation and carbon filtration samples. Some amplicon sequence variants related to potentially pathogenic genera were found in the DWTP. However, they were either not detected in the final water or in very low abundance (<2%), and all EU Directive quality standards were fully met. A combination of culture and high-throughput sequencing techniques may help DWTP managers to detect shifts in microbiome, allowing for a more in-depth assessment of operational performance. Full article

Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how desert plants have evolved unique developmental programs like having determinate meristems in the case of cacti while forming a branched and compact root system that allows efficient water uptake during wet periods. The remote germination mechanism in date palms is another example of developmental adaptation to survive in the dry and hot desert surface. Date palms have also designed non-gravitropic secondary roots, termed pneumatophores, to maximize water and nutrient uptake. Next, we highlight the distinct anatomical features developed by desert species in response to drought like narrow vessels, high tissue suberization, and air spaces within the root cortex tissue. Finally, we discuss the beneficial impact of the microbiome in promoting root growth in desert conditions and how these characteristics can be exploited to engineer resilient crops with a greater ability to deal with salinity induced by irrigation and with the increasing drought caused by global warming. Full article

Climate change has a massive impact on the global water cycle. Subsurface ecosystems, the earth largest reservoir of liquid freshwater, currently experience a significant increase in temperature and serious consequences from extreme hydrological events. Extended droughts as well as heavy rains and floods have measurable impacts on groundwater quality and availability. In addition, the growing water demand puts increasing pressure on the already vulnerable groundwater ecosystems. Global change induces undesired dynamics in the typically nutrient and energy poor aquifers that are home to a diverse and specialized microbiome and fauna. Current and future changes in subsurface environmental conditions, without doubt, alter the composition of communities, as well as important ecosystem functions, for instance the cycling of elements such as carbon and nitrogen. A key role is played by the microbes. Understanding the interplay of biotic and abiotic drivers in subterranean ecosystems is required to anticipate future effects of climate change on groundwater resources and habitats. This review summarizes potential threats to groundwater ecosystems with emphasis on climate change and the microbial world down below our feet in the water saturated subsurface. Full article