A natural 15N approach to determine the biological fixation of atmospheric nitrogen by biological soil crusts of the Negev Desert

Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops

Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared a similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared with those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All of the examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared with the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence the bacterial and diazotrophic community composition of any of these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced the community composition and function of these biocrusts.

Contrasting seasonal patterns and factors regulating biocrust N2-fixation in two Florida agroecosystems

Biocrusts are communities of microorganisms within the top centimeter of soil, often dominated by phototrophic dinitrogen-fixing (N₂-fixing) organisms. They are common globally in arid ecosystems and have recently been identified in agroecosystems. However, unlike natural ecosystem biocrusts, agroecosystem biocrusts receive regular fertilizer and irrigation inputs. These inputs could influence seasonal biocrust N₂-fixation and their relationship with soil nutrients in perennial agroecosystems, which is of particular interest given crop management requirements. In this study, biocrust and adjacent bare soil N₂-fixation activity was measured in the field during the summer, fall, spring, and winter seasons in a Florida citrus orchard and vineyard using both acetylene reduction assays and ¹⁵N₂ incubations. Samples were analyzed for microbial and extractable carbon (MBC, EC), nitrogen (MBN, EN), and phosphorus (MBP, EP). In both agroecosystems, biocrusts had greater microbial biomass and extractable nutrients compared to bare soil. The citrus and grape biocrusts were both actively fixing N₂, despite crop fertilization, with rates similar to those found in natural arid and mesic systems, from 0.1 to 142 nmol of C₂H₄ g^–1 of biocrust dry weight h^–1 (equivalent to 1–401 μmol m^–2h^–1). Lower soil temperatures and higher EC:EN ratios were associated with higher N₂-fixation rates in citrus biocrusts, while higher soil moisture and higher EP were associated with higher N₂-fixation rates in grape biocrusts. The N₂-fixation activity of these agroecosystem biocrusts indicates the possibility of biocrusts to enhance N cycling in perennial agroecosystems, with potential benefits for crop production.

Understanding changes in biocrust communities following phosphate mining in the Negev Desert

Biocrusts are key ecosystem engineers that are being destroyed due to anthropogenic disturbances such as trampling, agriculture and mining. In hyper-arid regions of the Negev Desert, phosphate has been mined for over six decades, altering the natural landscape over large spatial scales. In recent years, restoration-oriented practices were mandated in mining sites, however, the impact of such practices on the ecosystem, particularly the biocrust layer, has not been tested. Here, we evaluated post-mining biocrust bacterial communities and compared them to undisturbed (reference) biocrusts. We collected samples from four mining sites (each restored at a different year) and their corresponding reference sites. We hypothesized that post-mining bacterial communities would differ significantly from reference communities, given the slow regeneration of the biocrust. We also hypothesized that bacterial communities would vary among post-mining plots based on their restoration age. To test these hypotheses, we assessed the abundance and diversity of bacterial communities by sequencing the 16S rDNA and their photosynthetic potential by quantifying the abundance of cyanobacteria and chlorophyll a. The bacterial diversity was lower, and community composition differed significantly between post-mining and reference biocrusts. In addition, cyanobacteria abundances and chlorophyll a content were lower in post-mining biocrusts, indicating lower photosynthetic potential. However, no significant changes in bacterial communities were detected, regardless of the restoration age. We suggest that the practices implemented in the Negev mines may not support the recovery of the biocrust bacterial communities, particularly the cyanobacteria. Thus, active restoration measures are needed to accelerate the regeneration time of biocrusts at the hyper-arid Negev mines.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Climate stability and societal decline on the margins of the Byzantine empire in the Negev Desert

Understanding past human settlement of inhospitable regions is one of the most intriguing puzzles in archaeological research, with implications for more sustainable use of marginal regions today. During the Byzantine period in the 4^th century CE, large settlements were established in the arid region of the Negev Desert, Israel, but it remains unclear why it did so, and why the settlements were abandoned three centuries later. Previous theories proposed that the Negev was a “green desert” in the early 1^st millennium CE, and that the Byzantine Empire withdrew from this region due to a dramatic climatic downturn. In the absence of a local climate archive correlated to the Byzantine/Early Islamic transition, testing this theory has proven challenging. We use stable isotopic indicators of animal dietary and mobility patterns to assess the extent of the vegetative cover in the desert. By doing so, we aim to detect possible climatic fluctuations that may have led to the abandonment of the Byzantine settlements. The findings show that the Negev Desert was not greener during the time period under investigation than it is today and that the composition of the animals’ diets, as well as their grazing mobility patterns, remained unchanged through the Byzantine/Early Islamic transition. Favoring a non-climatic explanation, we propose instead that the abandonment of the Negev Byzantine settlements was motivated by restructuring of the Empire’s territorial priorities.

Possible nitrogen fertilization of the early Earth Ocean by microbial continental ecosystems

While significant efforts have been invested in reconstructing the early evolution of the Earth's atmosphere-ocean-biosphere biogeochemical nitrogen cycle, the potential role of an early continental contribution by a terrestrial, microbial phototrophic biosphere has been largely overlooked. By transposing to the Archean nitrogen fluxes of modern topsoil communities known as biological soil crusts (terrestrial analogs of microbial mats), whose ancestors might have existed as far back as 3.2 Ga ago, we show that they could have impacted the evolution of the nitrogen cycle early on. We calculate that the net output of inorganic nitrogen reaching the Precambrian hydrogeological system could have been of the same order of magnitude as that of modern continents for a range of inhabited area as small as a few percent of that of present day continents. This contradicts the assumption that before the Great Oxidation Event, marine and continental biogeochemical nitrogen cycles were disconnected.

Enhancing Non-symbiotic N2 Fixation in Agriculture

Much of the demand for nitrogen (N) in cereal cropping systems is met by using N fertilisers, but the cost of production is increasing and there are also environmental concerns. This has led to a growing interest in exploring other sources of N such as biological N2fixation. Non-symbiotic N2fixation (by free-living bacteria in soils or associated with the rhizosphere) has the potential to meet some of this need especially in the lower input cropping systems worldwide. There has been considerable research on non-symbiotic N2fixation, but still there is much argument about the amount of N that can potentially be fixed by this process largely due to shortcomings of indirect measurements, however isotope-based direct methods indicate agronomically significant amounts of N2fixation both in annual crop and perennial grass systems. New molecular technologies offer opportunities to increase our understanding of N2-fixing microbial communities (many of them non-culturable) and the molecular mechanisms of non-symbiotic N2fixation. This knowledge should assist the development of new plant-diazotrophic combinations for specific environments and more sustainable exploitation of N2-fixing bacteria as inoculants for agriculture. Whilst the ultimate goal might be to introduce nitrogenase genes into significant non-leguminous crop plants, it may be more realistic in the shorter-term to better synchronise plant-microbe interactions to enhance N2fixation when the N needs of the plant are greatest. The review explores possibilities to maximise potential N inputs from non-symbiotic N2fixation through improved management practices, identification of better performing microbial strains and their successful inoculation in the field, and plant based solutions.

Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae

Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4X^T. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4X^T displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C_15∶0, C_16∶1ω5c, summed feature 3 (containing C_16∶1ω6c and/or C_16∶1ω7c) and summed feature 4 (comprising anteiso-C_17∶1B and/or iso-C_17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4X^T actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4X^T is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4X^T ( = CCTCC AB 2013049^T = NRRL B-59974^T).

Diversity of free-living nitrogen-fixing microorganisms in wastelands of copper mine tailings during the process of natural ecological restoration

Biological nitrogen fixing is an important source of nitrogen input in the natural ecological restoration of mine wastelands. The diversity of nifH genes in tailings samples under different plant communities in Yangshanchong and Tongguanshan wastelands in Tongling, was analyzed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach. The nitrogen-fixing microorganism community in the upper layer of tailings of Tongguanshan wasteland discarded in 1980 showed higher Shannon-Wiener diversity index than that in Yangshanchong wasteland discarded in 1991. The diversity of nifH genes in Yangshanchong wasteland of copper mine tailings did not display a consistent successional tendency with development of plant communities during the process of natural ecological restoration. Phylogenetic analysis of 25 sequences of nifH gene fragments retrieved from the DGGE gels indicated that there were mainly two taxa of free-living nitrogen-fixing microorganisms, Proteobacteria and Cyanobacteria living in the wastelands investigated, most of which were unique and uncultured. Canonical correspondence analysis (CCA) based on the relationship between band patterns of DGGE profile and physico-chemical properties of tailings samples showed that the diversity of nifH genes in different tailing samples was mainly affected by loss of ignition, water content, pH and available Zn contents of wastelands. The dominant plant species and development period of plant communities by ameliorating pH, reducing the toxicity of heavy metals, increasing organic matter and water content affected the diversity and structure of the free-living nitrogen-fixing microorganisms in wastelands of copper mine tailings.