scholarly journals Changes in microbial community phylogeny and metabolic activity along the water column uncouple at near sediment aphotic layers in fjords

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales

AbstractFjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial community structure and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. Previous studies do not consider both prokaryotic and eukaryotic communities when linking metabolic potential and activity, community composition, and environmental gradients. To address this gap we profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing). Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter input than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between community structure and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

2021 ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales

Abstract Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. We profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing) to link metabolic potential, activity, and community composition to known community drivers. Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter imput than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between phylogeny and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.


2020 ◽  
Author(s):  
Louis J.P. Dufour ◽  
Anke. M. Herrmann ◽  
Julie Leloup ◽  
Cédric Przybylski ◽  
Luc Abbadie ◽  
...  

<p>It has recently been suggested that microbial-derived material is an important constituent of soil organic matter, and accumulation of organic matter in soil is related to microbial activity and the composition of the microbial communities present. However, microbial activity is generally intimately related to the properties of the carbon substrate (e.g. molecular diversity, energy content) available for decomposition. It is important, therefore, to understand in more detail what the drivers of microbial activity and their associated metabolic pathways are: the composition of the microbial communities or the properties of the available organic substrate.</p><p>Water extractable organic matter from 6 different grassland and forest soils were added cross-wise to samples of each of the soils. The total heat dissipation was measured by isothermal calorimetry during a 23 h incubation period. Heat dissipation is a measure of total metabolic activity in the soil. The total CO<sub>2</sub> emission was also determined, by gas chromatography-mass spectrometry. The elemental composition of low molecular weight organic substances (LMWOS) was obtained by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry, which allowed us to calculate the Nominal Oxidation State of Carbon (NOSC) from each exact molecular mass detected. The NOSC is related to the energy content of the molecules. The microbial composition was determined by 16S rRNA gene sequencing. This experimental design allowed us to evaluate potential links between microbial community composition and their metabolic pathways when different LMWOS are undergoing decomposition.</p><p>First, we found that the total heat dissipated and CO<sub>2</sub> emitted were associated with differences in the composition of LMWOS, independent of microbial community composition in the soil. We observed that the median of the total CO<sub>2</sub> emission was positively correlated with the weighted sum of the NOSC of each detected LMWOS. These results emphasise that a supply in available substrate with lower energy density (i.e. higher NOSC) may result in an increase in decarboxylation processes. Furthermore, total heat dissipated but not CO<sub>2</sub> was positively correlated to the molecular richness of LMWOS. This indicates that substrate with a higher molecular richness include also other metabolic pathways where CO<sub>2</sub> is not a decomposition end-product. Finally, we observed three different dynamics of heat dissipation during the 23 h incubation period. These dynamics were related to the microbial communities, but were independent of the LMWOS composition. The dynamic of heat dissipation were summarised by a Q<sub>t50</sub> index, i.e. the time required to release half of the heat dissipated in 23 h. The Q<sub>t50</sub> index was significantly correlated to the relative abundance of different bacterial taxa. In conclusion, whilst the short-term dynamics of substrate use appear to be associated with microbial community composition, the overall activity is more closely related to the composition of the available substrate.</p>


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Xiaomei Chen ◽  
Muying Liu ◽  
Zhanying Xu ◽  
Hui Wei

Abstract Climate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.


2020 ◽  
Author(s):  
Rachel hasler ◽  
Mark pawlett ◽  
Jim harris ◽  
Helen bostock ◽  
Marc redmile-gordon

<p>The type of soil organic amendment selected can have profound implications for carbon cycling processes in soils. Understanding the link between this choice and its effect on the soil microbiome will improve our understanding of the capacity of these materials to improve carbon sequestration and cycling dynamics. Understanding and facilitating the lifestyle strategies of microorganisms processing organic matter is essential to improving our understanding of the terrestrial carbon cycle. This research focuses on utilising organic amendments to alter the indigenous soil microbial community composition and function to improve the capacity of the soil to cycle and store carbon in horticultural soils.  The effects of annual application of various organic fertilisers (peat, bracken, bark, horse manure, garden compost) in a long-term (10year) field experiment were explored. Sampling was completed pre and post application of organic matter within one season (following 10 years of applications) to identify which organic amendment was more effective in producing benefits to plants through improved soil organic matter and which amendments provide the greatest legacy effect on carbon cycling. The response of the soil microbial community composition (phospholipid fatty acid analysis) and carbon functional cycling dynamics (respiration using MicroResp™) were determined with a view to improving our understanding of the interaction between the materials applied and microbial processes. PCA of the MicroResp™ data identified that all treatments had a different functional profile compared to the control[PM1]  with peat being significantly different from all other treatments. Horse manure and bark differed significantly within a single growing season; prior and post organic matter addition in spring 2019.  Microbial biomass measurements for garden compost and horse manure were significantly higher following organic matter addition compared to all other treatments and the control[PM2] .  All treatments had a significant effect [PM3] on hot water extractable carbon and total carbon. Peat had a significantly different effect[PM4] , when compared to other treatments, on the soil PLFA profile and bark application significantly increased [PM5] the neutral lipid (NLFA) biomarker 16:1ω5.  Bark and horse manure application both significantly increased PLFA fungal biomarker 18:2ω6,9. No significant differences were found between the fungal/bacterial ratios of the organic matter additions prior to being added to the soil. These findings show that altering the resources available to the soil microbial community has a significant impact on soil microbial community composition and microbially mediated carbon cycling functionality. Increasing our understanding of how soil functions are altered by land management decisions will enable better informed predictions of the long-term benefits of organic matter applications on carbon sequestration and cycling dynamics.</p>


PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6854 ◽  
Author(s):  
Zhigang Li ◽  
Kaiyang Qiu ◽  
Rebecca L. Schneider ◽  
Stephen J. Morreale ◽  
Yingzhong Xie

Background Addition of organic amendments has been commonly adopted as a means to restore degraded soils globally. More recently, the use of woody organic amendments has been recognized as a viable method of capturing and retaining water and restoring degraded and desertified soil, especially in semi-arid regions. However, the impacts of woody amendments on soil microbial community structure, versus other traditional organic supplements is less understood. Methods Three locally available natural organic materials of different qualities, i.e., cow manure (CM), corn straw (CS), and chipped poplar branches (PB) were selected as treatments in Ningxia, Northern China and compared with control soils. Four microcosms served as replicates for each treatment. All treatments contained desertified soil; treatments with amendments were mixed with 3% (w/w) of one of the above organic materials. After 7 and 15 months from the start of the experiment, soil samples were analyzed for chemical and physical properties, along with biological properties, which included microbial α-diversity, community structure, and relative abundance of microbial phyla. Results Both bacterial and fungal α-diversity indices were weakly affected by amendments throughout the experimental period. All amendments yielded different microbial community compositions than the Control soils. The microbial community composition in the CS and PB treatments also were different from the CM treatment. After 15 months of the experiment, CS and PB exhibited similar microbial community composition, which was consistent with their similar soil physical and chemical properties. Moreover, CS and PB also appeared to exert similar effects on the abundance of some microbial taxa, and both of these treatments yield different abundances of microbial taxa than the CM treatment. Conclusion New local organic amendment with PB tended to affect the microbial community in a similar way to the traditional local organic amendment with CS, but different from the most traditional local organic amendment with CM in Ningxia, Northern China. Moreover, the high C/N-sensitive, and lignin and cellulose decompose-related microbial phyla increased in CS and PB have benefits in decomposing those incorporated organic materials and improving soil properties. Therefore, we recommend that PB should also be considered as a viable soil organic amendment for future not in Ningxia, but also in other places.


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