scholarly journals The diversity and functional capacity of microbes associated with coastal phototrophs

2022 ◽  
Author(s):  
Khashiff K Miranda ◽  
Brooke L Weigel ◽  
Emily Fogarty ◽  
Iva A Veseli ◽  
Anne Giblin ◽  
...  
Keyword(s):  
Zostera Marina ◽  
Inorganic Nitrogen ◽  
Vitamin B ◽  
Metagenomic Sequencing ◽  
Carbon And Nitrogen ◽  
Functional Capabilities ◽  
Metabolic Functions ◽  
Coastal Marine ◽  
Nearshore Ecosystems ◽  
Marine Angiosperms

Coastal marine phototrophs exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their phototroph hosts through metabolisms that are unique to microbial taxa. Here we characterized the metabolic functions of phototroph-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.) and the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 72 metagenome assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic gene content. All host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis. Additionally, we found a range of nitrogen metabolism genes that transform dissolved inorganic nitrogen into forms that may be more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms, and contributes to the functional capabilities of microbes and their influence on carbon and nitrogen cycling in nearshore ecosystems.

scholarly journals Changes of Soil Microbes Related with Carbon and Nitrogen Cycling after Long-Term CO2 Enrichment in a Typical Chinese Maize Field

2020 ◽  
Vol 12 (3) ◽  
pp. 1250 ◽  
Author(s):  
Tiantian Diao ◽  
Zhengping Peng ◽  
Xiaoguang Niu ◽  
Rongquan Yang ◽  
Fen Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
Nitrogen Cycling ◽  
Relative Abundance ◽  
Soil Microbes ◽  
Inorganic Nitrogen ◽  
Ammonia Oxidizing Bacteria ◽  
Rhizospheric Soil ◽  
Carbon And Nitrogen ◽  
Carbon And Nitrogen Cycling ◽  
Maize Field

Elevated atmospheric CO2 concentration (eCO2) has been the most important driving factor and characteristic of climate change. To clarify the effects of eCO2 on the soil microbes and on the concurrent status of soil carbon and nitrogen, an experiment was conducted in a typical summer maize field based on a 10-year mini FACE (Free Air Carbon Dioxide Enrichment) system in North China. Both rhizospheric and bulk soils were collected for measurement. The soil microbial carbon (MBC), nitrogen (MBN), and soil mineral N were measured at two stages. Characteristics of microbes were assayed for both rhizospheric soil and bulk soils at the key stage. We examined the plasmid copy numbers, diversities, and community structures of bacteria (in terms of 16s rRNA), fungi (in terms of ITS-internal transcribed spacer), ammonia oxidizing bacteria (AOB) and denitrifiers including nirK, nirS, and nosZ using the Miseq sequencing technique. Results showed that under eCO2 conditions, both MBC and MBN in rhizospheric soil were increased significantly. The quantity of ITS was increased in the eCO2 treatment compared with that in the ambient CO2 (aCO2) treatment, while the quantity of 16s rRNA in rhizospheric soil showed decrease in the rhizospheric soil in the eCO2 treatment. ECO2 changed the relative abundance of microbes in terms of compositional proportion of some orders or genera particularly in the rhizospheric soil-n particular, Chaetomium increased for ITS, Subgroups 4 and 6 increased for 16s rRNA, Nitrosospira decreased for AOB, and some genera showed increase for nirS, nirK, and nosZ. Nitrate N was the main inorganic nitrogen form at the tasseling stage and both quantities of AOB and denitrifiers, as well as the nosZ/(nirS+nirK) showed an increase under eCO2 conditions particularly in the rhizospheric soil. The Nitrosospira decreased in abundance under eCO2 conditions in the rhizospheric soil and some genera of denitrifiers also showed differences in abundance. ECO2 did not change the diversities of microbes significantly. In general, results suggested that 10 years of eCO2 did affect the active component of C and N pools (such as MBC and MBN) and both the quantities and relative abundance of microbes which are involved in carbon and nitrogen cycling, possibly due to the differences in both the quantities and component of substrate for relevant microbes in the rhizospheric soils.

scholarly journals Actively restored ecosystems as a refuge for biological diversity: A case study from eelgrass (Zostera marina L.)

2015 ◽  
Author(s):  
Jonathan Lefcheck ◽  
Scott R Marion ◽  
Robert J Orth
Keyword(s):  
Zostera Marina ◽  
Biological Diversity ◽  
Trophic Levels ◽  
Critical Element ◽  
Invertebrate Community ◽  
Western Atlantic ◽  
Goods And Services ◽  
Nearshore Ecosystems ◽  
General Decline ◽  
Seagrass Cover

As nearshore ecosystems are increasingly degraded by human activities, active restoration is a critical element in ensuring the continued provision of goods and services by coastal habitats. Since 1997, over 1800 ha of the foundational species eelgrass (Zostera marina L.) has been reestablished in the coastal bays of the mid-western Atlantic. Here, we follow the functional recovery of the epifaunal invertebrate community associated with a restored eelgrass habitat from 2001-2013. Epifauna provide critical services by removing fouling epiphytes from eelgrass blades and transferring energy to higher trophic levels. After less than a decade, the invertebrate community in the restored bed was richer, more even, and exhibited greater variation in functional traits than a nearby natural bed. Analysis of environmental and physical data using random forests revealed the primary drivers of these differences was the increasing area and density of the restored bed directly attributable to both ongoing restoration efforts, and expansion from the initial planting efforts. Given that restored eelgrass now make up 32% of total seagrass cover in the mid-Atlantic, this restoration may foster regional biodiversity by providing new and pristine habitat, particularly given the general decline of natural eelgrass in this region and globally.

scholarly journals Effects of carbon and nitrogen sources on production of proteases by Bacillus subtilis IC-5

2018 ◽  
Vol 44 (2) ◽  
pp. 285-292
Author(s):  
Sereen Gul ◽  
Mujeeb Ur Rahman ◽  
Mohammad Ajmal ◽  
Abdul Kabir Khan Achakzai ◽  
Asim Iqbal
Keyword(s):  
Bacillus Subtilis ◽  
Sodium Nitrate ◽  
Inorganic Nitrogen ◽  
Carbon Sources ◽  
Basal Medium ◽  
Nitrogen Sources ◽  
Neutral Protease ◽  
Carbon And Nitrogen Sources ◽  
Inorganic Nitrogen Source ◽  
Carbon And Nitrogen

The effects of various carbon and nitrogen sources were evaluated on production of proteases by Bacillus subtilis IC-5. Both type and concentration of carbon and nitrogen sources influenced the production of proteases. Among the carbon sources glucose was found to be the most effective. It gave maximum production at 2% w/v concentration i.e., 1875 and 950 U/ml, alkaline and neutral protease, respectively. The response of Bacillus subtilis IC-5 towards synthesis and excretion of enzymes varied with the type of nitrogen sources. The addition of organic nitrogen sources to basal medium repressed the synthesis of proteases while the addition of inorganic nitrogen source such as sodium nitrate was found to be the best stimulating for alkaline and neutral protease synthesis. Sodium nitrate enhanced the production up to 62.40 and 10.52% of alkaline and neutral protease, respectively against w.r.t. control.

scholarly journals Patterns and persistence of hydrologic carbon and nutrient export from collapsing upland permafrost

2015 ◽  
Vol 12 (12) ◽  
pp. 3725-3740 ◽  
Author(s):  
B. W. Abbott ◽  
J. B. Jones ◽  
S. E. Godsey ◽  
J. R. Larouche ◽  
W. B. Bowden
Keyword(s):  
Aquatic Ecosystems ◽  
Inorganic Nitrogen ◽  
The Arctic ◽  
Nutrient Export ◽  
Initial Pulse ◽  
Dissolved Carbon ◽  
Carbon And Nitrogen ◽  
The North ◽  
North Slope Of Alaska ◽  
High Concentrations

Abstract. As high latitudes warm, vast stocks of carbon and nitrogen stored in permafrost will become available for transport to aquatic ecosystems. While there is a growing understanding of the potential effects of permafrost collapse (thermokarst) on aquatic biogeochemical cycles, neither the spatial extent nor temporal duration of these effects is known. To test hypotheses concerning patterns and persistence of elemental export from upland thermokarst, we sampled hydrologic outflow from 83 thermokarst features in various stages of development across the North Slope of Alaska. We hypothesized that an initial pulse of carbon and nutrients would be followed by a period of elemental retention during feature recovery, and that the duration of these stages would depend on feature morphology. Thermokarst caused substantial increases in dissolved organic carbon and other solute concentrations with a particularly large impact on inorganic nitrogen. Magnitude and duration of thermokarst effects on water chemistry differed by feature type and secondarily by landscape age. Most solutes returned to undisturbed concentrations after feature stabilization, but elevated dissolved carbon, inorganic nitrogen, and sulfate concentrations persisted through stabilization for some feature types, suggesting that aquatic disturbance by thermokarst for these solutes is long-lived. Dissolved methane decreased by 90% for most feature types, potentially due to high concentrations of sulfate and inorganic nitrogen. Spatial patterns of carbon and nutrient export from thermokarst suggest that upland thermokarst may be a dominant linkage transferring carbon and nutrients from terrestrial to aquatic ecosystems as the Arctic warms.

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