Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment

He, Changfei; Liu, Jihua; Wang, Rui; Li, Yuanning; Zheng, Qiang; Jiao, Fanglue; Shi, Quan; Xu, Yongle; Zhang, Rui; Thomas, Helmuth; Batt, John; Hill, Paul S.; Lewis, Marlon R.; Maclntyre, Hugh; Lu, Longfei; Zhang, Qinghua; Tu, Qichao; Shi, Tuo; Chen, Feng; Jiao, Nianzhi

doi:10.1016/j.watres.2022.118281

Cited by 22 publications

(6 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Those are still used nowadays to study marine particles or POC degradations (e.g. Jiao et al 2018;Zhang et al 2021;He et al 2022). Such large-scale controlled experiments can bridge the gap between small-scale experiments and in situ measurements (Conover and Paranjape 1977;Robinson et al 2018).…”

Section: Lab Experimental Set Upsmentioning

confidence: 99%

A focus on different types of organic matter particles and their significance in the open ocean carbon cycle

Baumas¹,

Bižić²

2024

Preprint

View full text Add to dashboard Cite

Marine particles are key to the cycling of major elements on Earth and play an important role in the balance of nutrients in the ocean. Three main categories of marine particles link the different parts of the open ocean by shaping carbon distribution: (i) Sinking; (ii) Suspended, and (iii) Ascending. Atmospheric carbon captured by phytoplankton in the surface water, is partly sequestered by sinking particles to the bottom of the ocean, having an important role in controlling global climate. Suspended particles represent a major substrate of organic carbon for heterotrophic microorganisms, being more likely to get remineralized. Ascending particles, depending on their content, point of origin, and ascending velocity, may lead to carbon remineralization in the upper layers of the ocean in closer proximity to the atmosphere. Marine particles are hotspots of microbial activity and thus heavily colonized by microorganisms whose dynamics play an important role in organic matter degradation, aggregation and sinking, thus, directly influencing the biological carbon pump efficiency. Microbiomes of marine particles differ depending on particle size, source, and age. Nevertheless, these factors are generally overlooked, and particles are mostly studied as "bulk" without considering the high heterogeneity between individual particles. This hinders our understanding of the carbon budget in the ocean and thus future predictions of climate change. In this review we discuss characteristics of known particle-types and associated sampling methods. We further identify gaps in knowledge and highlight the need to better understand the single particles ecosystem to improve upscaling rates to the global scale.

show abstract

Section: Lab Experimental Set Upsmentioning

confidence: 99%

A focus on different types of organic matter particles and their significance in the open ocean carbon cycle

Baumas¹,

Bižić²

2024

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, there are some metabolites that can be produced by only a few species (Figure 2) (Table S1), etc. For example, terpineol can be produced by Oenococcus oeni, providing reference information for the synthetic pathways of terpenoids and steroids in microorganisms of Cupei [32]. Riboflavin produced by…”

Section: Metabolite Transport Network Of Microbiota In Shanxi Aged Vi...mentioning

confidence: 99%

Microbial Metabolic Interaction in Fermentation Ecosystem and Cooperation in Flavor Compounds Formation of Chinese Cereal Vinegar

Wu,

Liu,

Liu

et al. 2024

Food Science and Human Wellness

View full text Add to dashboard Cite

Shanxi aged vinegar (SAV) is a famous cereal vinegar in China, which is produced through a solid-state fermentation where diverse microbes spontaneously and complex interactions occur. Here, combined with the metatranscriptomics, the microbial co-occurrence network was constructed, indicating that Lactobacillus, Acetobacter and Pediococcus are the most critical genera to maintain the fermentation stability. Based on an extensive collection of 264 relevant literatures, a transport network containing 2271 reactions between microorganisms and compounds was constructed, showing that glucose (84% of all species), fructose (67%) and maltose (67%) are the most frequently utilized substrates while lactic acid (64%), acetic acid (45%) are the most frequently occurring metabolites. Specifically, the metabolic influence of species pairs was calculated using a mathematical calculation model and the metabolic influence network was constructed. The topology properties analysis found that Lactobacillus was the key role with robust metabolic control of vinegar fermentation ecosystem and acetic acid and lactic acid were the main metabolites with feedback regulation in microbial metabolism of SAV. Furthermore, systematic coordination of positive and negative impacts was proved to be inevitable to form flavor compounds and maintain a natural microbial ecosystem. This study provides a new perspective for understanding microbial interactions in fermented food.

show abstract

“…When the surrounding environment changes, the microbial community also undergoes changes, which subsequently alter the metabolic pathways in these microbes (Gianoulis et al 2009). These changes in the microbial metabolic pathways are more sensitive than the changes in the community structure (He et al 2022;Li et al 2018). Long-term interactions occur among the macroalgae, shell sh, and degrading microbial communities.…”

Section: Introductionmentioning

confidence: 99%

“…have suggested that bacteria have the potential to convert unstable leucine and into carboxyl-rich alicyclic molecules (CRAM)(He et al 2022). CRAMs collectively represent a group of organic compounds that are rich in carboxyl groups and fused aliphatic rings, and these have been characterized and form a major portion of the RDOM library(Hertkorn et al 2006).…”

mentioning

confidence: 99%

Microbial degradation of DOC released by the mixed culture of Crassostrea gigas and Undaria pinnatifida

Hu,

Su,

Shao

et al. 2024

Preprint

View full text Add to dashboard Cite

To determine the potential of shellfish-algae aquaculture on carbon sequestration, we studied the microbial degradation process of dissolved organic carbon (DOC) released in a mixed culture of Crassostrea gigas and Undaria pinnatifida. The results showed that DOC concentration tended to rapidly decline followed by a slow decline period and then a steady phase with 28% concentration of DOC remaining over a period of 120 days after removing the Crassostrea gigas and Undaria pinnatifida. Bacterial community structure was dynamic over time and changed in response to three stages of DOC degradation. In the three stages of DOC degradation, the dominant microbial classes shifted from Alphaproteobacteria (39%) and Gammaproteobacteria (43%) in the rapid decline period to Planctomycetia (28%) and Flavobacteria (19%) in the slow decline period to Alphaproteobacteria (29%) in the stable period. The amino acid metabolism and carbohydrate metabolism were observed to be highly active in the rapid DOC decline and slow DOC decline periods, respectively. The carbon-fixing genes smtA and rbcL were most abundant during the DOC rapid degradation stage. The DOC concentration was significantly negatively correlated with Planctomycetia, Anaerolineae (p < 0.05) and the tricarboxylic acid cycle (TCA cycle) (p < 0.001). These results suggested that the main carbon fixation pathways TCA cycle and its related carbon-fixing genes may be involved in the degradation of DOC released by the mixed culture of shellfish-algae.

show abstract

Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment

Cited by 22 publications

References 81 publications

A focus on different types of organic matter particles and their significance in the open ocean carbon cycle

A focus on different types of organic matter particles and their significance in the open ocean carbon cycle

Microbial Metabolic Interaction in Fermentation Ecosystem and Cooperation in Flavor Compounds Formation of Chinese Cereal Vinegar

Microbial degradation of DOC released by the mixed culture of Crassostrea gigas and Undaria pinnatifida

Contact Info

Product

Resources

About