Community differences and potential function along the particle size spectrum of microbes in the twilight zone

Abstract

Background: The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.

Results: Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.

Conclusion: Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.

Keywords: Community differences; Ecological function; Prokaryotes; Twilight zone.

Fig. 1

Map of the sampling habitats used in this study. “1” represents Longqi station, located in the Southwest Indian Ocean (SWIO); “2” and “3” represent Haima and Site F stations, respectively, in the northern South China Sea (NSCS); and “4” represents the South East Asian Time-series Study (SEATS) station in the South China Sea

Fig. 2

Composition and diversity of prokaryotic communities among the different sampling regions. A Taxonomic composition at the order level with a minimum of 1% of the total sequences. In the sample names, the uppercase letters denote the station names, such that S, H, F, and L indicate SEATS, Haima, Site F, and Longqi, respectively. The second number indicates the sampling depth, and the third number represents the particle size fraction. B nMDS ordination based on the Bray–Curtis dissimilarity, showing the clustering of different size fractions (left) and water depth (right) at the order level. The samples are color-coded accordingly. Significant clusters were determined by ANOSIM (9999 permutations, p < 0.01). NSCS indicates Haima and Site F sampling stations, whereas SWIO indicates Longqi sampling site. C The Shannon index of the prokaryotic community according to the fraction size (left) and water depth (right) in the different sampling regions

Fig. 3

A An UpSet plot illustrating the distribution of taxonomic groups across the three sampling regions. The black circles and vertical lines represent the intersections between taxonomic groups corresponding to each vertical bar. Petal diagrams showing the number of genera shared among B the different size fractions and C the water depths. NSCS indicates Haima and Site F, whereas SWIO indicates Longqi

Fig. 4

Distinct patterns of the prokaryotic co-occurrence networks in the three sampling regions. A Co-occurrence network analysis of the three regions. The size of the nodes corresponds to their rank order of degree. The nodes are connected by pink or green edges, which indicate significantly positive or negative relationships (estimated by Spearman’s correlation with a significance level of 0.01), respectively. The absolute values of the correlation coefficients represent the correlation strength, such that thicker edges indicate stronger correlations. B Network topological parameters for these habitats. NSCS indicates Haima and Site F, whereas SWIO indicates Longqi

Fig. 5

Z-score heatmap boxes showing A prokaryotic central carbon metabolic process genes and B organic carbon degradation-related genes in the different size fractions and water depths of the three regions. In A, “WL pathway” indicates genes of the Wood-Ljungdahl pathway of acetogenesis, and “CO” indicates carbon monoxide processing genes. NSCS represents Haima and Site F, whereas SWIO represents Longqi. The source data are listed in Table S7

Fig. 6

Z-score heatmap boxes showing the functional genes involved in the phosphorus, methane, sulfur, and nitrogen cycles (based on the KEGG database) in the different A size fractions and B water depths of the three regions. NSCS represents Haima and Site F, whereas SWIO represents Longqi

Fig. 7

Phylogenetic tree constructed from the 122 retrieved MAGs. The outer layers of the tree indicate (from inside to outside) the color codes of the various bacterial phyla, as well as the percentage completeness, contamination, GC content, and genome size of each MAG

Fig. 8

Composition and diversity of the carbohydrate-active enzymes (CAZyme) in each MAG across the microbial taxa. A Boxplots showing the total CAZy gene count per MAG within each phylum (green) and the CAZyme functional diversity (i.e., number of CAZy families per MAG; red). The boxplots indicate the median values as well as the lower and upper quartiles, and the numbers in brackets on the y-axis denote the MAG count. All the CAZymes belonging to the AA, CBM, PL, CE, GH, and GT classes were considered. B Distribution of CAZymes across the MAGs of six major bacterial phyla. AA, auxiliary activities; CBM, cellulose-binding motifs; CE, carbohydrate esterases; GH, glycosyl hydrolases; GT, glycosyltransferase; and PL, polysaccharide lyases